Bend the pins in the harness you’re using more towards the center; I bet they’re just slightly out of making contact when using it on that particular board giving you an issue. I’ll strongly bet your start button inputs aren’t making contact with this particular board.
I had this problem occur recently with my P1 Button 1 not registering on one of my CPS2 setups and using a small jewelers screwdriver to bend the pins closer towards the center of the harness solved my problem.