Somehow, it sounds like the computer is not registering flipper button presses. Step one is to go into dedicated switch test mode, and make sure that when you push a flipper button, the flipper button switch itself lights up. My guess is that it won't. Sadly, I don't have that flipper setup in front of me right this moment, so I can't tell you if it's on your board or your switches. I don't think it's a short, as that would make the flippers be on all the time. It may be a failed component. The easiest way to tell would be to swap the current flipper board with a known good one, and see what happens.