Paul,
Joystick up stopped working on me while I was having my best run so far. I see up being registered in WinVice. This was at the begging of a new level.
I also couldn't pull out a bomb - but I threw up a rope.
I let the timer run out so the ghost could get me... then a button press wouldn't bring me back to the menu to start a new game.
Would a VICE snapshot file help for debugging? I saved one when it started acting weird. If you'd like the file just let me know how I can get it to you.