Don't worry, you're not missing anything in terms of Ending C, the chest ending is kind of intended to be a little bit confusing! It becomes a little clearer on subsequent loops.
Sorry to hear to got a bug in the lever room! It seems to work okay when I try it, but the whole thing has quite a lot of moving parts so, that is probably the number 1 place I'd expect things to break in unexpected ways. Once the jam is over I'll probably tinker with that room some more.