Help with setting special permissions

I use Windows XP Professional and NTFS file system.

In order to make certain folders on the non-system partition inaccessible to other users, I have been setting special permissions to those folders. But I have had problems when I had to reinstall the OS on some systems. The folders I had protected would not even be accessible to me! Is there a solution to this?

In my case all I want to do is to make certain folders inaccessible to other users and yet keep the properties of nested folders inside unchanged.