Given that the whole control panel isn't working, I'd suspect the common ground wire is the problem, but it sounds like you checked that. Make sure the ground connector pin at the JAMMA board is making contact, probably a good idea to clean all the fingers on the board with a fiberglass pen and hit them with contact cleaner, see if that clears it up.
Beyond that, verify that you're getting 5v from the power supply to the board. If that's good and you have continuity from the control panel switches to the edge connector, the simplest thing would be just to spring for a new ~$35 60-in-1 board. I wouldn't waste time troubleshooting one of those boards when a replacement is easy and cheap.
If the power supply isn't putting out a steady 5v, replace that.