What i would try:
1. delete everything in your user/condition zero folder, EXCEPT czero, and in czero delete everything besides the game folders, i.e., maps/models/wads/etc. (den start up the game and let steam rebuild the missing files.
2. i would just completely uninstall/reinstall cz. it's not that big and will reinstall in 3 seconds, just of course again, backup your maps/models/sprites/models/etc if you have anything important in der.
3. Fuck with the registry? idk if you can delete these values in the registry like you can with hammer, and since i know so little about regediting, i'd try this last.