In the end, we had problems with WinCache too. Latest version did resolved the language pack update issue and trying a single course backup & restore did work too. However, when teacher began to dupplicate activities, they sometime had a php error regarding a folder that cannot be empty because it was locked by another process (cannot remember exact error). That seem very similar to the languages issues we had and disabling and re-enabling WinCache in IIS resolved the problem... until it happen again. So, we move to XCache instead and didn't had any issues since then. It been more than a month now and everythings run fine.
Also, we had unexpected IIS crashes sometime, once a month maybe, sometime more. Server was still up and running and no error got into PHP logs or EV, but pages just seem to stop being processed. Since we use XCache, these problems seem to have disapeared too. I cannot for sure relate these two however, but it sure look like a strange coincidence. No users have complain about performance either so, switching the PHP Accelerator to XCache help us a lot.