As far as I know the issue has not been really solved yet. Neither there has been any feedback from any M$ guy as well.
In my case, I narrowed down the problem to those assemblies that contain textual resources such as embedded javaScript files, which are loaded from client via the WebResource or ScriptResource handler. Other assemblies that do not contain such resources have never caused the error until now.
I wonder what makes assemblies with javascript or other resources that difficult to keep being loaded correctly by the CLR!?
Has somebody faced similar issues yet?