Have you made any changes to the application start methods (e.g. ~/App_Code/Application/CMSAppBase.cs file)? What happens if you use the same Global.ascx file you were using previously? Is your application still running despite this error being logged when hitting CMS Desk? Could you try copying your DLLs files directly from the upgrade package then clearing the .NET cache?
Please let me know if I can be of further assistance.