Just to clarify - the rest of the game worked fine, but pressing either joystick to the right did nothing? Did you do anything else besides reseat the CPU before it started working?
The joysticks are just switches, and these feed into chips on the small I/O board. The CPU reads all the joystick inputs the same way, so it doesn't make sense that reseating it would fix two specific lines not working. And if there was a problem with one of the CPU pins, the game probably would not have booted successfully.
Any info would help .. I can't stand unsolved mysteries ..
Yes, the other thing I did was move around the two ribbon cables. And I believe I also reseated the smaller ribbon cable to the I/O board. Thanks for all the responses, I will now know where to start when it happens again.