@koro, yeah the nub configuator will fix the problem, but I'll explain what happened.
So... mupen64 and some other PNDs use the NUBs in joystick mode. There is a script when these PNDs start up that sets the PNDs into Joystick mode and there is a script when the PND closes that sets the nubs back to the prior setting (usually mouse mode for most people). So If the program crashes or is closed abruptly the script at the end never ran so it never reverts the nubs back into mouse mode.