Windows XP pseudo corrupted files

Hi guys!

For ages I have this problem with clients backups after a format and clean install (NTFS file system):
When using some third part software to backup and restore the files of a client, some files - most of then actually - are classified as corrupted by Windows, but if I try to access, copy, move or delete them using some Linux distro, I can do it with no problem. It happens with any type of file .jpg, .xls, .ods, .zip any type. And every time when Windows is starting the chkdsk tool begins to check the file system (even using chkntfs /d after the restart).
I understand that if the user protects his/her account with a password it could happen and the sollution is just to change the owner of the files/folders. The problem is most of the users don't protect their users.
So, what could be done to solve this, knowing that the files are not really corrupted?
Does it have anything to do with the SID, HWID?