I've found the culprit and its the Cross Uni BOS uniform mod- when console spawning, for example, Sarge with the mod on makes it invisible, but when turned off its visible again. So I turned it off then loaded a save game and slept for 4 days straight hoping this would clear up all the glitched copies, but then in the Old Castle mission I still had the problem. If I have to revert back to a two days old save I'll feel like killing myself. Hence I ask of you brethren, tell me a way to reset all the robots so they are good again :'(