Please, files don't reinstall or copy themselves automatically. It is you that is doing something wrong.
You mentioned somewhere you had Vista right? Vista has some problems about file placement when you install the game and mods to certains folders ('C:\Program Files' if i'm not mistaken) so that's the most likely cause of your "supernatural" installs. Anyway this problem when using BC under Vista has been mentioned around here various times already, so if you bother to do the search function you'll most likely find better awnsers than mine to it.