Hi "dadaneo"
According to my experience "jv16 PT 2012" is in the normal mode of "Clean and fix my Computer" extremely aggressive with file extensions.
See pictures:
Themepack 2.PNG
Themepack 1.PNG
As I said before it happened to me some weeks ago that I killed with "PT" the file association for Win7 theme packs. Luckily I found the corresponding backups and recovered the whole thing.
Since that happening I recovered all backed up file extensions and put them into the ignore list which paid off as a good move. There had been some more extensions which I really need.
So I hope for you that you still have a good backup.
OK, that development was a bit past the limit.
Therefore I don't understand that nobody from the team seems to be caring about this problem.