Yeah, the Mutators stay the way I put them. I *think* I found the causes of the crashing on ending, at least for me. I went through my Mutators activating them one by one, and then ending the mission. It didn't crash until I activated DS9FX. Of course it didn't start crashing every time until I installed Ftech. So there might be a conflict there? I'm going to try DS9FX with Ftech's mutator turned off and see if it crashes then.
Edit: Nope, still crashes with Ftech off and DS9FX on, but does not crash with only Ftech on.
Edit2: It seems I fixed the WalkFX key mapping. I reset the keys so they weren't mapped. Then I remapped them and shut down the game. (with DS9FX off, so It didn't crash.) Then I restarted BC and the keys have stayed mapped like they should.