The touch detection is handled in the background with a threaded polling loop, right back in the Cap1xxx library. I'd wager that's where something is going wrong, since exiting before cleanly stopping a thread can cause all sorts of woes.
There should be a Python "atexit" handler function registered to prevent this, but clearly things aren't being handled in the order they should, or something has been overlooked.
I think the logical next step would be to try and recreate this using just the Cap1xxx library directly, then we can narrow it down to the right thing. I'll tuck it on the end of my TODO list.