Wow, that is pretty crazy. But I'm wondering if permissions is really the cause. Usually permissions issues would represent themselves with "access denied" errors....
Anyway, the permisssions for the groups that I have for c:\windows\system32 (default) are:
TrustedInstaller
- special permissions that are not inherited with all Allow check boxes checked and permissions applied to "This folder and subfolders"
SYSTEM
- special permissions that are not inherited with all Allow check boxes checked EXCEPT Full Control, Delete subfolders and files, Change permissions, and Take ownership check boxes checked and permissions applied to This folder only
SYSTEM
- special permissions that are not inherited with all Allow check boxes checked and permissions applied to Subfolders and files only
Administrators
- special permissions that are not inherited with all Allow check boxes checked EXCEPT Full Control, Delete Subfolders and Files, Change Permissions, and Take Ownership check boxes checked and permissions applied to This folder only
Administrators
- special permissions that are not inherited with all Allow check boxes checked and permissions applied to Subfolders and files only
USERS
- special permissions that are not inherited with only the following Allow check boxes checked -- Traverse folder / execute file, List folder / read data, Read Attributes, Read extended attributes, and Read permissions check boxes checked and permissions applied to This folder, subfolders, and files
CREATOR OWNER
- special permissions that are not inherited with all Allow check boxes checked and permissions applied to Subfolders and files only
And if those don't do the trick, you can throw in the "Everyone" group for giggles but that's about all I can think of