I am surprised that the assembly caching does not work. We never experienced such problems on our online demos. I suppose that you already checked that, but in any case, could you double check that the Telerik assemblies were properly upgraded and deployed on the server? Usually the compiler does not complain if you mix the assembly versions of the referenced Telerik assemblies, but in runtime exceptions are thrown.
I experimented with modifying the extmap.xml files - tried to include the version number in the downloadUri attribute, but unfortunately this didn't work. You could experiment with this approach.
Another idea that just came to my mind is to deploy the XAP and ZIP files to a folder, named after the application version (or the date). This way the ZIP files will be automatically referenced to the relative path, containing the version/date and the cache should work. To avoid keeping many folders you could rewrite the requests to the versioned folders.
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