Ok more time spent on this. Not much progress. This is what I did: 

Stripped all unused modules from the initial site. This left me with:

 

• DotNetNuke Web Application Framework 04.09.00  
• [Skin Objects] Skin Objects are User Controls which can be used to provide custom functionality to your Skin files.   
• Account Login Allows users to login to the portal. 01.00.00 
• Help The Help Module renders tutorials in a structured manner and allows for easy navigation of the tutorials. 03.00.02 
• IFrame The HTML iframe creates an inline frame that contains another document, which can be located on your or any other site. 04.04.00 
• Links This module renders a list of hyperlinks. Links includes an edit page, which allows authorized users to edit the Links data stored in the SQL database. 04.00.01 
• Map The core map module for DotNetNuke. 01.00.09 
• NB_Store_CategoryMenu Show and allows navigation of the categories in the store. 01.01.01 
• NB_Store_Checkout Used as the Store Cart and Checkout for clients. 01.01.01 
• NB_Store_GatewayPayPal PayPal Gateway Provider 02.00.01 
• NB_Store_ManagerMenu Store Manager Menu, allows management of all store functions. 01.01.01 
• NB_Store_MiniCart Displays Store Mini-Cart 01.01.01 
• NB_Store_OrderHistory Allows clients to view their orders. 01.01.01 
• NB_Store_ProductList Displays List of store products 01.01.01 
• NB_Store_Search Search Input module for NB_Store 01.01.01 
• Search Input The Search Input module provides the ability to submit a search to a given search results module. 01.00.00 
• Search Results The Search Reasults module provides the ability to display search results. 01.00.00 
• Text/HTML This module renders a block of HTML or Text content. The Html/Text module allows authorized users to edit the content either inline or in a separate administration page. The content is stored in the database. According to module settings, tokens can be used, that get replaced during display. 04.08.01 
• User Account Allows users to register and manage their account. 01.00.00 
• UsersOnline Users Online allows you to see who is online in your portal, and see membership counts 03.01.00 
• YetAnotherForumDotNet Add the YAF forum to your portal. 01.91.05 

 
Set Portal Skin and Admin Skin to <not specified>

Follow Wiki upgrade path:

Update to 4.9.5 - no errors
All works, checking modules
UsersOnline needs updating from 03.01.00 to 04.09.04 - done

Update to 5.4.4 
Executing Application Upgrades: 05.03.00 Error!
Executing Application Upgrades: 05.04.03 Error!
Installing Package File HTML_Community_05.04.03_Install:  Error!
Installing Package File Messaging_01.01.00_Install:  Error!
Installing Package File Taxonomy_01.01.00_Install:  Error!
Back to same issues as before with links like i.e. "login" and "register" not working

Rolled Back to 4.9.0 with module list as above
Follow upgrade path as recommended by Sebastian Leupold

Update to 5.2.3 - no errors
UsersOnline needs updating from 3.1.0 to 5.1.0 - can' update because links not working. 
Same issue with links not working

I was also wondering if something could be wrong with the web.config. This is the original one before the update: 

<configuration>
  <!-- register local configuration handlers -->
  <configSections>
    <sectionGroup name="dotnetnuke">
      <!-- the requirePermission attribute will cause a syntax warning - please ignore - it is required for Medium Trust support-->
      <section name="data" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="logging" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="scheduling" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="htmlEditor" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="navigationControl" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="searchIndex" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="searchDataStore" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="friendlyUrl" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="caching" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="authentication" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="members" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="roles" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
      <section name="profiles" requirePermission="false" type="DotNetNuke.Framework.Providers.ProviderConfigurationHandler, DotNetNuke" />
    </sectionGroup>
    <section name="yafnet" type="yaf.SectionHandler,yaf" />
  </configSections>
  <yafnet configSource="dnnyafnet.config" />
  <connectionStrings>
    <add name="SiteSqlServer" connectionString="Data Source=mssql2.openhost.net.nz;Initial Catalog=flaxbasket;User ID=******;Password=*******" />
  </connectionStrings>
  <appSettings>
    <!-- Connection String for SQL Server 2005 Express - kept for backwards compatability - legacy modules   -->
    <add key="SiteSqlServer" value="Data Source=mssql2.openhost.net.nz;Initial Catalog=flaxbasket;User ID=**********;Password=*******" />
    <!-- Connection String for SQL Server 2000/2005 - kept for backwards compatability - legacy modules
    <add key="SiteSqlServer" value="Server=(local);Database=DotNetNuke;uid=;pwd=;"/>
    -->
    <add key="InstallTemplate" value="DotNetNuke.install.config" />
    <add key="AutoUpgrade" value="true" />
    <add key="UseInstallWizard" value="true" />
    <add key="InstallMemberRole" value="true" />
    <add key="ShowMissingKeys" value="false" />
    <add key="EnableWebFarmSupport" value="false" />
    <add key="EnableCachePersistence" value="false" />
    <add key="HostHeader" value="" />
    <!-- Host Header to remove from URL so "www.mydomain.com/johndoe/Default.aspx" is treated as "www.mydomain.com/Default.aspx" -->
    <add key="RemoveAngleBrackets" value="false" />
    <!--optionally strip angle brackets on public login and registration screens-->
    <add key="PersistentCookieTimeout" value="0" />
    <!--use as persistent cookie expiration. Value is in minutes, and only active if a non-zero figure-->
    <!-- set UsePortNumber to true to preserve the port number if you're using a port number other than 80 (the standard)
    <add key="UsePortNumber" value="true" /> -->
    <add key="InstallationDate" value="3/24/2009" />
  </appSettings>
  <system.codedom>
    <compilers>
      <compiler language="vb" type="Microsoft.VisualBasic.VBCodeProvider, System, Version=2.0.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089" extension=".VB" />
    </compilers>
  </system.codedom>
  <!-- The system.webServer section is required for IIS7 compatability It is ignored by IIS6-->
  <system.web>
    <!-- Ensure validationkey is not set to AutoGenerate,IsolateApps so it correctly supports webfarms -->
    <machineKey validationKey="32EE3D0DCA11C5A88D4EE117A42D8AB242B81AD8" decryptionKey="C69BD624514E36031B5301B7D565F84C527FCADE7EF1D764" decryption="3DES" validation="SHA1" />
    <!-- HttpModules for Common Functionality -->
    <httpModules>
      <!-- add name="Authentication" type="DotNetNuke.HttpModules.AuthenticationModule, DotNetNuke.HttpModules.Authentication" / -->
      <add name="ScriptModule" type="System.Web.Handlers.ScriptModule, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      <add name="Compression" type="DotNetNuke.HttpModules.Compression.CompressionModule, DotNetNuke.HttpModules" />
      <add name="RequestFilter" type="DotNetNuke.HttpModules.RequestFilter.RequestFilterModule, DotNetNuke.HttpModules" />
      <add name="UrlRewrite" type="DotNetNuke.HttpModules.UrlRewriteModule, DotNetNuke.HttpModules" />
      <add name="Exception" type="DotNetNuke.HttpModules.Exceptions.ExceptionModule, DotNetNuke.HttpModules" />
      <add name="UsersOnline" type="DotNetNuke.HttpModules.UsersOnline.UsersOnlineModule, DotNetNuke.HttpModules" />
      <add name="DNNMembership" type="DotNetNuke.HttpModules.Membership.MembershipModule, DotNetNuke.HttpModules" />
      <add name="Personalization" type="DotNetNuke.HttpModules.Personalization.PersonalizationModule, DotNetNuke.HttpModules" />
    </httpModules>
    <httpHandlers>
      <!-- This is for CAPTCHA support -->
      <add verb="*" path="*.captcha.aspx" type="DotNetNuke.UI.WebControls.CaptchaHandler, DotNetNuke" />
      <!-- This is for Serving files, secure, insecure, from database -->
      <add verb="*" path="LinkClick.aspx" type="DotNetNuke.Services.FileSystem.FileServerHandler, DotNetNuke" />
      <!-- This adds syndication support -->
      <add verb="*" path="RSS.aspx" type="DotNetNuke.Services.Syndication.RssHandler, DotNetNuke" />
      <!-- This adds legacy support for the Logoff page -->
      <add verb="*" path="Logoff.aspx" type="DotNetNuke.Services.Authentication.LogOffHandler, DotNetNuke" />
      <!-- ASP.NET AJAX support -->
      <remove verb="*" path="*.asmx" />
      <add verb="*" path="*.asmx" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      <add verb="*" path="*_AppService.axd" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      <add verb="GET,HEAD" path="ScriptResource.axd" type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" validate="false" />
    </httpHandlers>
    <!-- set code access security trust level - this is generally set in the machine.config
    <trust level="Medium" originUrl=".*" />
     -->
    <!-- set debugmode to false for running application -->
    <compilation strict="false">
      <buildProviders>
        <remove extension=".resx" />
        <remove extension=".resources" />
      </buildProviders>
      <assemblies>
        <add assembly="Microsoft.VisualBasic, Version=8.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A" />
        <add assembly="System.DirectoryServices, Version=2.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A" />
        <add assembly="System.Design, Version=2.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A" />
        <add assembly="System.Management, Version=2.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A" />
        <add assembly="System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      </assemblies>
      <!-- register your app_code subfolders to generate granular assemblies during compilation
      <codeSubDirectories> 
         <add directoryName="sub-directory name"/> 
      </codeSubDirectories>
      -->
      <codeSubDirectories>
        <add directoryName="HTML" />
        <add directoryName="IFrame" />
      </codeSubDirectories>
    </compilation>
    <!-- permits errors to be displayed for remote clients -->
    <!-- Forms or Windows authentication -->
    <authentication mode="Forms">
      <forms name=".DOTNETNUKE" protection="All" timeout="60" cookieless="UseCookies" />
    </authentication>
    <!--
   <identity impersonate="true"/>
   <authentication mode="Windows">
   </authentication>
-->
    <!-- allow large file uploads -->
    <httpRuntime useFullyQualifiedRedirectUrl="true" maxRequestLength="8192" requestLengthDiskThreshold="8192" />
    <httpCookies httpOnlyCookies="true" requireSSL="false" domain="" />
    <!--  GLOBALIZATION
This section sets the globalization settings of the application. 
Utf-8 is not supported on Netscape 4.x 
If you need netscape compatiblity leave iso-8859-1.
UTF-8 is recommended for complex languages
-->
    <globalization culture="en-US" uiCulture="en-NZ" requestEncoding="UTF-8" responseEncoding="UTF-8" fileEncoding="UTF-8" />
    <!--<globalization culture="en-US" uiCulture="en"  fileEncoding="iso-8859-1" requestEncoding="iso-8859-1" responseEncoding="iso-8859-1"/>-->
    <!-- page level options -->
    <pages validateRequest="false" enableViewStateMac="true" enableEventValidation="false">
      <controls>
        <add tagPrefix="asp" namespace="System.Web.UI" assembly="System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      </controls>
      <namespaces>
        <add namespace="System.ComponentModel" />
        <add namespace="System.Data" />
        <add namespace="System.Data.SqlClient" />
        <add namespace="System.Drawing" />
        <add namespace="Microsoft.VisualBasic" />
        <add namespace="System.Globalization" />
        <add namespace="DotNetNuke.Services.Localization" />
        <add namespace="DotNetNuke.Entities.Users" />
        <add namespace="DotNetNuke" />
        <add namespace="DotNetNuke.Common" />
        <add namespace="DotNetNuke.Data" />
        <add namespace="DotNetNuke.Framework" />
        <add namespace="DotNetNuke.Modules" />
        <add namespace="DotNetNuke.Security" />
        <add namespace="DotNetNuke.Services" />
        <add namespace="DotNetNuke.UI" />
        <add namespace="DotNetNuke.Entities.Portals" />
        <add namespace="DotNetNuke.Common.Utilities" />
        <add namespace="DotNetNuke.Services.Exceptions" />
        <add namespace="DotNetNuke.Entities.Tabs" />
      </namespaces>
    </pages>
    <!-- ASP.NET 2 Membership/Profile/Role and AnonymousAuthentication Providers -->
    <!-- anonymousIdentification configuration:
          enabled="[true|false]"                              Feature is enabled?
          cookieName=".ASPXANONYMOUS"                         Cookie Name
          cookieTimeout="100000"                              Cookie Timeout in minutes
          cookiePath="/"                                      Cookie Path
          cookieRequireSSL="[true|false]"                     Set Secure bit in Cookie
          cookieSlidingExpiration="[true|false]"              Reissue expiring cookies?
          cookieProtection="[None|Validation|Encryption|All]" How to protect cookies from being read/tampered
          domain="[domain]"                                   Enables output of the "domain" cookie attribute set to the specified value
        -->
    <anonymousIdentification enabled="true" cookieName=".ASPXANONYMOUS" cookieTimeout="100000" cookiePath="/" cookieRequireSSL="false" cookieSlidingExpiration="true" cookieProtection="None" domain="" />
    <membership defaultProvider="AspNetSqlMembershipProvider" userIsOnlineTimeWindow="15">
      <providers>
        <clear />
        <!-- Configuration for DNNSQLMembershipProvider:
              connectionStringName="string"               Name corresponding to the entry in <connectionStrings> section where the connection string for the provider is specified
              passwordAttemptThreshold="int"              The number of failed password attempts, or failed password answer attempts that are allowed before locking out a user?s account
              passwordAttemptWindow="int"                 The time window, in minutes, during which failed password attempts and failed password answer attempts are tracked
              enablePasswordRetrieval="[true|false]"      Should the provider support password retrievals
              enablePasswordReset="[true|false]"          Should the provider support password resets
              requiresQuestionAndAnswer="[true|false]"    Should the provider require Q & A
       minRequiredPasswordLength="int"          The minimum password length
       minRequiredNonalphanumericCharacters="int"  The minimum number of non-alphanumeric characters
              applicationName="string"                    Optional string to identity the application: defaults to Application Metabase path
              requiresUniqueEmail="[true|false]"          Should the provider require a unique email to be specified
              passwordFormat="[Clear|Hashed|Encrypted]"   Storage format for the password: Hashed (SHA1), Clear or Encrypted (Triple-DES)
              description="string"                        Description of what the provider does
        -->
        <add name="AspNetSqlMembershipProvider" type="System.Web.Security.SqlMembershipProvider" connectionStringName="SiteSqlServer" enablePasswordRetrieval="true" enablePasswordReset="true" requiresQuestionAndAnswer="false" minRequiredPasswordLength="7" minRequiredNonalphanumericCharacters="0" requiresUniqueEmail="false" passwordFormat="Encrypted" applicationName="DotNetNuke" description="Stores and retrieves membership data from the local Microsoft SQL Server database" />
      </providers>
    </membership>
    <customErrors mode="Off" />
  </system.web>
  <runtime>
    <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
      <probing privatePath="bin;bin\HttpModules;bin\Providers;bin\Modules;bin\Support;" />
    </assemblyBinding>
  </runtime>
  <dotnetnuke>
    <htmlEditor defaultProvider="FckHtmlEditorProvider">
      <providers>
        <clear />
        <add name="FckHtmlEditorProvider" type="DotNetNuke.HtmlEditor.FckHtmlEditorProvider.FckHtmlEditorProvider, DotNetNuke.FckHtmlEditorProvider" providerPath="~/Providers/HtmlEditorProviders/Fck/" CustomConfigurationPath="~/Providers/HtmlEditorProviders/Fck/custom/FCKConfig.js" EnhancedSecurityDefault="false" SecureConfigurationPath="~/Providers/HtmlEditorProviders/Fck/custom/FCKConfigSecure.js" ImageGalleryPath="~/Providers/HtmlEditorProviders/Fck/fckimagegallery.aspx" ImageUploadPath="~/Providers/HtmlEditorProviders/Fck/fckimagegallery.aspx" ImageAllowedFileTypes="gif,png,bmp,jpg" FlashGalleryPath="~/Providers/HtmlEditorProviders/Fck/fckimagegallery.aspx" FlashUploadPath="~/Providers/HtmlEditorProviders/Fck/fckimagegallery.aspx" FlashAllowedFileTypes="fla,swf" LinksGalleryPath="~/Providers/HtmlEditorProviders/Fck/fcklinkgallery.aspx" DynamicStylesGeneratorPath="~/Providers/HtmlEditorProviders/Fck/FCKStyles.aspx" DynamicStylesCaseSensitive="true" DynamicStylesGeneratorFilter="controlpanel|filemanager|mainmenu|wizard" StaticStylesFile="~/Providers/HtmlEditorProviders/Fck/FCKeditor/fckstyles.xml" StylesDefaultMode="dynamic" DynamicCSSGeneratorPath="~/Providers/HtmlEditorProviders/Fck/FCKCSS.aspx" StaticCSSFile="~/Providers/HtmlEditorProviders/Fck/FCKeditor/editor/css/fck_editorarea.css" CSSDefaultMode="dynamic" spellCheck="ieSpell" AvailableToolbarSkins="Office2003,Silver" DefaultToolbarSkin="Office2003" AvailableToolBarSets="DNNDefault,Default,NoGallery,Basic" DefaultToolbarSet="DNNDefault" DefaultImageGallerySkin="Default" DefaultFlashGallerySkin="Default" DefaultLinksGallerySkin="Default" FCKDebugMode="false" UseFCKSource="false" OptionsOpenMode="ShowModalDialog" ShowModuleType="true" FixOldDNNPostback="false" CustomOptionsDialog="Admin" />
      </providers>
    </htmlEditor>
    <navigationControl defaultProvider="SolpartMenuNavigationProvider">
      <providers>
        <clear />
        <add name="SolpartMenuNavigationProvider" type="DotNetNuke.NavigationControl.SolpartMenuNavigationProvider, DotNetNuke.SolpartMenuNavigationProvider" providerPath="~\Providers\NavigationProviders\SolpartMenuNavigationProvider\" />
        <add name="DNNMenuNavigationProvider" type="DotNetNuke.NavigationControl.DNNMenuNavigationProvider, DotNetNuke.DNNMenuNavigationProvider" providerPath="~\Providers\NavigationProviders\DNNMenuNavigationProvider\" />
        <add name="DNNTreeNavigationProvider" type="DotNetNuke.NavigationControl.DNNTreeNavigationProvider, DotNetNuke.DNNTreeNavigationProvider" providerPath="~\Providers\NavigationProviders\DNNTreeNavigationProvider\" />
        <add name="DNNDropDownNavigationProvider" type="DotNetNuke.NavigationControl.DNNDropDownNavigationProvider, DotNetNuke.DNNDropDownNavigationProvider" providerPath="~\Providers\NavigationProviders\DNNDropDownNavigationProvider\" />
        <add name="ASP2MenuNavigationProvider" type="DotNetNuke.NavigationControl.ASP2MenuNavigationProvider, DotNetNuke.ASP2MenuNavigationProvider" providerPath="~\Providers\NavigationProviders\ASP2MenuNavigationProvider\" />
      </providers>
    </navigationControl>
    <searchIndex defaultProvider="ModuleIndexProvider">
      <providers>
        <clear />
        <add name="ModuleIndexProvider" type="DotNetNuke.Services.Search.ModuleIndexer, DotNetNuke.Search.Index" providerPath="~\Providers\SearchProviders\ModuleIndexer\" />
      </providers>
    </searchIndex>
    <searchDataStore defaultProvider="SearchDataStoreProvider">
      <providers>
        <clear />
        <add name="SearchDataStoreProvider" type="DotNetNuke.Services.Search.SearchDataStore, DotNetNuke.Search.DataStore" providerPath="~\Providers\SearchProviders\SearchDataStore\" />
      </providers>
    </searchDataStore>
    <data defaultProvider="SqlDataProvider">
      <providers>
        <clear />
        <add name="SqlDataProvider" type="DotNetNuke.Data.SqlDataProvider, DotNetNuke.SqlDataProvider" connectionStringName="SiteSqlServer" upgradeConnectionString="" providerPath="~\Providers\DataProviders\SqlDataProvider\" objectQualifier="" databaseOwner="dbo" />
      </providers>
    </data>
    <logging defaultProvider="DBLoggingProvider">
      <providers>
        <clear />
        <add name="XMLLoggingProvider" type="DotNetNuke.Services.Log.EventLog.XMLLoggingProvider, DotNetNuke.XMLLoggingProvider" configfilename="LogConfig.xml.resources" providerPath="~\Providers\LoggingProviders\XMLLoggingProvider\" />
        <add name="DBLoggingProvider" type="DotNetNuke.Services.Log.EventLog.DBLoggingProvider.DBLoggingProvider, DotNetNuke.Provider.DBLoggingProvider" providerPath="~\Providers\LoggingProviders\Provider.DBLoggingProvider\" />
      </providers>
    </logging>
    <scheduling defaultProvider="DNNScheduler">
      <providers>
        <clear />
        <add name="DNNScheduler" type="DotNetNuke.Services.Scheduling.DNNScheduling.DNNScheduler, DotNetNuke.DNNScheduler" providerPath="~\Providers\SchedulingProviders\DNNScheduler\" debug="false" maxThreads="1" />
      </providers>
    </scheduling>
    <friendlyUrl defaultProvider="DNNFriendlyUrl">
      <providers>
        <clear />
        <add name="DNNFriendlyUrl" type="DotNetNuke.Services.Url.FriendlyUrl.DNNFriendlyUrlProvider, DotNetNuke.HttpModules" includePageName="true" regexMatch="[^a-zA-Z0-9 _-]" />
      </providers>
    </friendlyUrl>
    <caching defaultProvider="FileBasedCachingProvider">
      <providers>
        <clear />
        <add name="FileBasedCachingProvider" type="DotNetNuke.Services.Cache.FileBasedCachingProvider.FBCachingProvider, DotNetNuke.Caching.FileBasedCachingProvider" providerPath="~\Providers\CachingProviders\FileBasedCachingProvider\" />
        <add name="BroadcastPollingCachingProvider" type="DotNetNuke.Services.Cache.BroadcastPollingCachingProvider.BPCachingProvider, DotNetNuke.Caching.BroadcastPollingCachingProvider" providerPath="~\Providers\CachingProviders\BroadcastPollingCachingProvider\" />
      </providers>
    </caching>
    <authentication defaultProvider="ADSIAuthenticationProvider">
      <providers>
        <clear />
        <add name="ADSIAuthenticationProvider" type="DotNetNuke.Authentication.ActiveDirectory.ADSI.ADSIProvider, DotNetNuke.Authentication.ActiveDirectory" providerPath="~\Providers\AuthenticationProviders\ADSIProvider\" />
      </providers>
    </authentication>
    <members defaultProvider="AspNetMembershipProvider">
      <providers>
        <clear />
        <add name="AspNetMembershipProvider" type="DotNetNuke.Security.Membership.AspNetMembershipProvider, DotNetNuke.Provider.AspNetProvider" providerPath="~\Providers\MembershipProviders\AspNetMembershipProvider\" />
      </providers>
    </members>
    <roles defaultProvider="DNNRoleProvider">
      <providers>
        <clear />
        <add name="DNNRoleProvider" type="DotNetNuke.Security.Membership.DNNRoleProvider, DotNetNuke.Provider.DNNProvider" providerPath="~\Providers\MembershipProviders\DNNMembershipProvider\" />
      </providers>
    </roles>
    <profiles defaultProvider="DNNProfileProvider">
      <providers>
        <clear />
        <add name="DNNProfileProvider" type="DotNetNuke.Security.Profile.DNNProfileProvider, DotNetNuke.Provider.DNNProvider" providerPath="~\Providers\MembershipProviders\DNNMembershipProvider\" />
      </providers>
    </profiles>
  </dotnetnuke>
  <system.webServer>
    <!-- The system.webServer section is required for IIS7 compatability It is ignored by IIS6-->
    <modules>
      <add name="ScriptModule" type="System.Web.Handlers.ScriptModule, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" preCondition="managedHandler" />
      <add name="Compression" type="DotNetNuke.HttpModules.Compression.CompressionModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
      <add name="RequestFilter" type="DotNetNuke.HttpModules.RequestFilter.RequestFilterModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
      <add name="UrlRewrite" type="DotNetNuke.HttpModules.UrlRewriteModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
      <add name="Exception" type="DotNetNuke.HttpModules.Exceptions.ExceptionModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
      <add name="UsersOnline" type="DotNetNuke.HttpModules.UsersOnline.UsersOnlineModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
      <add name="DNNMembership" type="DotNetNuke.HttpModules.Membership.MembershipModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
      <add name="Personalization" type="DotNetNuke.HttpModules.Personalization.PersonalizationModule, DotNetNuke.HttpModules" preCondition="managedHandler" />
    </modules>
    <handlers>
      <clear />
      <add name="Plesk_Handler_0-270494962" path="*.asp" verb="GET,HEAD,POST,TRACE" modules="IsapiModule" scriptProcessor="c:\windows\system32\inetsrv\asp.dll" resourceType="Either" />
      <add name="Plesk_Handler_0-270494679" path="*.cer" verb="GET,HEAD,POST,TRACE" modules="IsapiModule" scriptProcessor="c:\windows\system32\inetsrv\asp.dll" resourceType="Either" />
      <add name="Plesk_Handler_0-270494678" path="*.asa" verb="GET,HEAD,POST,TRACE" modules="IsapiModule" scriptProcessor="c:\windows\system32\inetsrv\asp.dll" resourceType="Either" />
      <add name="Plesk_Handler_0-270494677" path="*.cdx" verb="GET,HEAD,POST,TRACE" modules="IsapiModule" scriptProcessor="c:\windows\system32\inetsrv\asp.dll" resourceType="Either" />
      <add name="Plesk_Handler_0-270494674" path="*.ashx" verb="GET,HEAD,POST,DEBUG" type="System.Web.UI.SimpleHandlerFactory" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494673" path="*.asmx" verb="GET,HEAD,POST,DEBUG" type="System.Web.Services.Protocols.WebServiceHandlerFactory, System.Web.Services, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494672" path="*.aspx" verb="GET,HEAD,POST,DEBUG" type="System.Web.UI.PageHandlerFactory" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494666" path="*.rem" verb="GET,HEAD,POST,DEBUG" type="System.Runtime.Remoting.Channels.Http.HttpRemotingHandlerFactory, System.Runtime.Remoting, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494663" path="*.soap" verb="GET,HEAD,POST,DEBUG" type="System.Runtime.Remoting.Channels.Http.HttpRemotingHandlerFactory, System.Runtime.Remoting, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494633" path="*.shtm" verb="GET,POST" modules="ServerSideIncludeModule" resourceType="Either" />
      <add name="Plesk_Handler_0-270494632" path="*.shtml" verb="GET,POST" modules="ServerSideIncludeModule" resourceType="Either" />
      <add name="Plesk_Handler_0-270494631" path="*.stm" verb="GET,POST" modules="ServerSideIncludeModule" resourceType="Either" />
      <add name="Plesk_Handler_0-270494630" path="WebResource.axd" verb="GET,DEBUG" type="System.Web.Handlers.AssemblyResourceLoader" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494629" path="trace.axd" verb="GET,HEAD,POST,DEBUG" type="System.Web.Handlers.TraceHandler" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494628" path="WebAdmin.axd" verb="GET,DEBUG" type="System.Web.Handlers.WebAdminHandler" scriptProcessor="C:\Windows\Microsoft.NET\Framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="AJAX_ScriptResourceHandler" path="ScriptResource.axd" verb="GET,HEAD" type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="AJAX_AppServiceHandler" path="*_AppService.axd" verb="*" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="AJAX_WebServiceHandler" path="*.asmx" verb="*" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="LogoffHandler*" path="Logoff.aspx" verb="*" type="DotNetNuke.Services.Authentication.LogOffHandler, DotNetNuke" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="RSSJandler" path="RSS.aspx" verb="*" type="DotNetNuke.Services.Syndication.RssHandler, DotNetNuke" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="LinkClickHandler" path="LinkClick.aspx" verb="*" type="DotNetNuke.Services.FileSystem.FileServerHandler, DotNetNuke" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="CaptchaHandler" path="*.captcha.aspx" verb="*" type="DotNetNuke.UI.WebControls.CaptchaHandler, DotNetNuke" resourceType="Unspecified" preCondition="integratedMode,runtimeVersionv2.0" />
      <add name="rules-Integrated" path="*.rules" verb="*" type="System.ServiceModel.Activation.HttpHandler, System.ServiceModel, Version=3.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="Plesk_Handler_0-270494619" path="*.rules" verb="*" modules="IsapiModule" scriptProcessor="c:\windows\microsoft.net\framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="xoml-Integrated" path="*.xoml" verb="*" type="System.ServiceModel.Activation.HttpHandler, System.ServiceModel, Version=3.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="Plesk_Handler_0-270494616" path="*.xoml" verb="*" modules="IsapiModule" scriptProcessor="c:\windows\microsoft.net\framework\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494614" path="*.svc" verb="*" modules="IsapiModule" scriptProcessor="%systemroot%\microsoft.net\framework64\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="svc-Integrated" path="*.svc" verb="*" type="System.ServiceModel.Activation.HttpHandler, System.ServiceModel, Version=3.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="TraceHandler-Integrated" path="trace.axd" verb="GET,HEAD,POST,DEBUG" type="System.Web.Handlers.TraceHandler" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="WebAdminHandler-Integrated" path="WebAdmin.axd" verb="GET,DEBUG" type="System.Web.Handlers.WebAdminHandler" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="AssemblyResourceLoader-Integrated" path="WebResource.axd" verb="GET,DEBUG" type="System.Web.Handlers.AssemblyResourceLoader" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="PageHandlerFactory-Integrated" path="*.aspx" verb="GET,HEAD,POST,DEBUG" type="System.Web.UI.PageHandlerFactory" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="SimpleHandlerFactory-Integrated" path="*.ashx" verb="GET,HEAD,POST,DEBUG" type="System.Web.UI.SimpleHandlerFactory" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="HttpRemotingHandlerFactory-rem-Integrated" path="*.rem" verb="GET,HEAD,POST,DEBUG" type="System.Runtime.Remoting.Channels.Http.HttpRemotingHandlerFactory, System.Runtime.Remoting, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="HttpRemotingHandlerFactory-soap-Integrated" path="*.soap" verb="GET,HEAD,POST,DEBUG" type="System.Runtime.Remoting.Channels.Http.HttpRemotingHandlerFactory, System.Runtime.Remoting, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" resourceType="Unspecified" preCondition="integratedMode" />
      <add name="Plesk_Handler_0-270494594" path="*.axd" verb="GET,HEAD,POST,DEBUG" modules="IsapiModule" scriptProcessor="%windir%\microsoft.net\framework64\v2.0.50727\aspnet_isapi.dll" resourceType="Unspecified" />
      <add name="TRACEVerbHandler" path="*" verb="TRACE" modules="ProtocolSupportModule" resourceType="Unspecified" />
      <add name="Plesk_Handler_0-270494579" path="*.dll" verb="*" modules="IsapiModule" resourceType="File" requireAccess="Execute" allowPathInfo="true" />
      <add name="Plesk_Handler_0-270494578" path="*.exe" verb="*" modules="CgiModule" resourceType="File" requireAccess="Execute" allowPathInfo="true" />
      <add name="StaticFile" path="*" verb="*" modules="StaticFileModule,DefaultDocumentModule,DirectoryListingModule" resourceType="Either" />
    </handlers>
    <validation validateIntegratedModeConfiguration="false" />
  </system.webServer>
</configuration>

 

Can you see anything obviously wrong with it? 

 

It's frequently annoyed me that the upgrade process says (for example like Peter's)...

Executing Application Upgrades: 05.03.00 Error!
Executing Application Upgrades: 05.04.03 Error!
Installing Package File HTML_Community_05.04.03_Install: Error!
Installing Package File Messaging_01.01.00_Install: Error!
Installing Package File Taxonomy_01.01.00_Install: Error!

...but gives no useful clue about what the problem is. Is there anywhere that the actual error is logged? That would give vital clues about what's gone wrong.

@Sebastian - I'm hoping you might know this, or might know someone who does know.

@Peter - In the absence of any useful information in the log. ISTM that we know a virgin install will upgrade (well it will for me). So it's either something to do with your configuration, or the modules you have. Fortunately you have a testbed. Try this. Uninstall ALL the additional modules you have on there. Yes I know that loses your customer etc data but bear with me.

If that bare install will upgrade then we can point the finger at the modules. If it won't then it's something deeper about the basic install and it's settings (or the modules have rubbish uninstalls that leave dangerous junk behind).

If that upgrade works then repeat uninstalling all but one, then repeat uninstalling all but two, etc, until you find the one (maybe ones) that break the upgrade.

One configuration issue that I know causes trouble, I don't know if it breaks upgrades though, is having a site with the US language disabled.

http://www.dnnsoftware.com/forums/forumid/197/threadid/461188/scope/posts/threadpage/4

You have to read a long way down.

One

---

Best wishes,
- Richard
Agile Development Consultant, Practitioner, and Trainer
www.dynamisys.co.uk