That is worth testing, the program is mean to run under an admin account as a standard user wont have the permissions for the repairs to run.
So when the permissions repairs run it first goes and sets full permissions for administrator and system and such to all the files and folders, it has to do this so that it has the permissions to restore the defaults. After that is ran the defaults are restored. This would only restore the defaults that are in the file, any extra folders and such would still have the full permissions set for administrator and system.
1 sec let me go double check the code.
Looks like I do have users set to full access, I changed this a while ago but this one section didnt get the change. So when the defaults are put back those are removed but only on those files and folders, not any new ones not in the defaults.
The best thing to do is to just remove users from it all togeather, of course the only downfall would be any permissions that need to set for standard users, but I dont think that happens very often, would be a lot better to just remove users from it, then it will only be these
TrustedInstaller
Administrators
System
ALL APPLICATION PACKAGES
Shane