It cant be the system or applications replicating them since I just took a bunch of old pictures(jpg's) I had, renamed them with the .old ext. and then placed them all over.
Also, I dont have uac enabled, so running it in Admin mode would mean nothing(I think). Also, since the .bat file removes some of the .old files but not all, there is not where the problem is. Not sure why that happens
-Edit-
Just tried running it as admin, and then the cmd window barely appears, then dissapear without removing any files..??