I've just upgraded a site to 5.1.4 (can't go more recent than that, I'm on SQL2000)  and all went well apart from one error which was the "Cannot insert duplicate key row in object 'Packages' with unique index 'IX_Packages'. The statement has been terminated." error.  A check in Gemini suggested that this error was ignorable so I've allowed the system to stand

However, whilst all looks good on the surface, I'm seeing lots of these errors in the log:

AssemblyVersion: 5.1.4
PortalID: 0
PortalName: MyDomain
UserID: 8
UserName: BarryS
ActiveTabID: 77
ActiveTabName: Contacts
RawURL: /Home/Contacts.aspx
AbsoluteURL: /Default.aspx
AbsoluteURLReferrer: http://www.domain.com/AreaMeetings/Bordeaux/Introduction.aspx
UserAgent: Opera/9.80 (Windows NT 6.0; U; en-GB) Presto/2.5.22 Version/10.51
DefaultDataProvider: DotNetNuke.Data.SqlDataProvider, DotNetNuke.SqlDataProvider
ExceptionGUID: 214470f7-a2f1-4433-9e74-6ce554f41306
InnerException: PackageID
FileName:
FileLineNumber: 0
FileColumnNumber: 0
Method: System.Data.ProviderBase.FieldNameLookup.GetOrdinal
StackTrace:
Message: System.IndexOutOfRangeException: PackageID at System.Data.ProviderBase.FieldNameLookup.GetOrdinal(String fieldName) at System.Data.SqlClient.SqlDataReader.GetOrdinal(String name) at System.Data.SqlClient.SqlDataReader.get_Item(String name) at DotNetNuke.Entities.Modules.DesktopModuleInfo.Fill(IDataReader dr) at DotNetNuke.Common.Utilities.CBO.FillObjectFromReader(Object objObject, IDataReader dr)
Source:
Server Name: WEB912

Anyone have a clue how to fix this?

Thanks Mitchel,

I did have one error in the logs to do with duplicate entries in the Packages index, but my investigations of reported errors led me to believe that it could be ignored.  I have since rolled back to 4.9.5, and will start on a process of upgrading all the modules that I use to the latest versions that will work with 5.1.4, and then doing test installs to see if the same errors are generated when viewing the pages that caused them last time.