Well, the good news is rebuilding the level from my source has proven to correct the problem. The problem is of course everything needs to be rebuilt. This isn't a huge deal just some editor grunt work. Things need to be moved over from the old level one at a time, reset, and then tested to ensure they haven't broken the game. Still, the game seems pretty good at this point, definitely a lot of work to do (right now the enemies are pretty brutal), but we're on our way!