Phu, we finally found the cause for this issue... It was all about a missing HttpHandlers-entry in
web.config for the ScriptResource.axd. The final hint was found in http://blogs.telerik.com/blogs/posts/08-07-18/web_resources_demystified_part_3_troubleshooting.aspx
under "Dealing with the 404 error code (the requested URL was not found)", even if we didn't get a 404.
FYI: A similar issue is discussed here: http://forums.asp.net/t/1009084.aspx