They have ways of knowing man. They might have added security to the game since it was leaked. So for the people who have the backup version they won't have that security code and there they can see.

No one knows for sure if you are or aren't running a copy/backup. I personally believe it has something to do with the license. If two or more people have a matching license it flags you and your console. It's just like cd keys and pc games. However I could be entirely wrong, but it seems rather logical don't ya think? And it's not really a scare tactic because people have been getting banned for running backups etc.