I have a mature 4.x web site that has gone thru the upgrade process to the latest version. With that I have created several custom modules.  I keep receiving errors in the form of "updatepanel is ambuguous in the namespace System.Web.UI".  This has been plaguing me for months until I did a line-by-line comparison of the web.config and found the following entries on my development system that does not exist in any of the other sites. Subsequently adding the following fixed my problems.  If you're having this issue modify your Web.Config with the following runtime entry.

<runtime>
  <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
    <probing privatePath="bin;bin\HttpModules;bin\Providers;bin\Modules;bin\Support;" />
    <dependentAssembly>
       <assemblyIdentity name="System.Web.Extensions" publicKeyToken="31bf3856ad364e35" />
       <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0" />
    </dependentAssembly>
    <dependentAssembly>
      <assemblyIdentity name="System.Web.Extensions.Design" publicKeyToken="31bf3856ad364e35" />
      <bindingRedirect oldVersion="1.0.0.0-1.1.0.0" newVersion="3.5.0.0" />
    </dependentAssembly>
  </assemblyBinding>
</runtime>

Jon