running pygame in a thread and then killing it and restarting it multiple times is not a well tested path. I would expect that is why you you are running into weird and unusual problems. Also note, the various platforms (PC, Mac, Linux) often have their own odd problems with running window management code in multiple threads - just a note if cross-platformness is important to you.
Practically speaking, what you probably want to do is: a) find another way to do what you want without shutting down and restarting pygame and possibly without a separate thread even. b) treat this as a pygame bug - i.e. try to make a minimal sample that demonstrates the problem for somebody (possibly even you) to use for debugging.
Should I not be running pygame in a thread then killing it and
restarting it multiple times in the same process? I assume if this was
bad I'd see more random problems than this.