Custom Content and Mod issues

Hi, I've discovered a problem with my game. I first off have backed up my CC onto a thumbdrive and deleted it on my PC completely. But I'm still having problems with the enable mods and enable script mods being checked. I've repaired the game multiple times but no luck. Has anyone else run across this problem? Apparently my folder doesn't have a locaclthumbcache either, I'm at my wits end with this