Button "down" doesn't go through the microcontroller, but directly to the JAMMA game, so this would suggest some problems with the actual PCB game? Try other boards. Also, what controller do you use?JusI unplugged the controller and plug it back in and button 3 works but then down didn’t work.
Dirty JAMMA connector? Try other games and let me know.sometimes I don’t get any blue, if I remove the HAS and then reseat it on the jamma edge it usually comes back. There’s been once where it didn’t work the 1st time but the 2nd time reattaching it worked.

Even re-capped them to be in sharp state when the time comes! Got Haunted Castle PCB, Neo Geo MVS with multicart and IGS PGM with 3 Cave shooters just waiting here...
I have TMNT and Sunset Riders. The Sunset Riders came in a converted TMNT cabinet.