Thanks very much everyone. Even though Sfaizst's program wasn't designed to fix these new issues, somehow running it would make the levels work properly after completing the level you changed the gamemode on. However, simply using Hunter's suggestion of restarting the level "/r", and not running any fix program worked perfectly - all enemies appear and the rotating objects are back.

I'm still wondering how to fix the clipping through solid objects issue though (passing through crates, rocks), if anyone has a comment on that. Also I notice there is a server option to set the MAX possible resolution of the connecting clients' windows. I know how to use that command, but I'm wondering how to actually set my own game's resolution manually myself.

I know, it's a slippery subject, since people can use it to see out of standard range, but I'm not really interested in using that method, or playing on public servers anyway (and it seems any server running JJ2+ can also limit their res). I would just like some thoughts on how you would change the res manually (doing it in places like single-player, or in campaign coop doesn't seem harmful right?).

Thanks again