Check that the correct version of the Telerik.Web.UI.dll was installed into the site's \bin folder. It should be version 2010.01.0309.35. It is possible that that the assembly file might not have overwritten the older version that was already in the 5.3.1 site's \bin folder.

If the correct version of the Telerik.Web.UI.dll assembly was not installed, you can obtain it from the Telerik_05.04.00_Install.zip package found in the DotNetNuke_Community_05.04.01_Upgrade.zip package's \Install\Module\ folder.

Also, check that the site's web.config file contains the following section:

<dependentAssembly xmlns="urn:schemas-microsoft-com:asm.v1"> 
        <assemblyIdentity name="Telerik.Web.UI" publicKeyToken="121fae78165ba3d4" />

        <!--Upgraded by DotNetNuke.Telerik.Web version 5.4.0 - Date: xx/xx/xx xxx:xx PM-->

 

        <!--<bindingRedirect oldVersion="2007.1.1.20-2011.4.2000.20" newVersion="2009.3.1104.35" xmlns="urn:schemas-microsoft-com:asm.v1" />-->

        <bindingRedirect oldVersion="2008.0.0.0-2020.0.0.0" newVersion="2010.01.309.35" />
</dependentAssembly>

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Bill, WESNet Designs
Team Lead - DotNetNuke Gallery Module Project (Not Actively Being Developed)
Extensions Forge Projects . . .
Current: UserExport, ContentDeJour, ePrayer, DNN NewsTicker, By Invitation
Coming Soon: FRBO-For Rent By Owner

tried to upgrade 5.5.0 to 5.6.0 also had this error at first, fixed it all and then... well still had a lot of errors...