Did some more testing. Its not the boards. In mame 64.. not sure which version but I haven't changed it since i built it over 6 months ago.. it never happens. Works perfectly.
but in either Launchbox or BigBox it will do it even after I installed the latest update. once it happened, I tried a few things. I unplugged the control stick from the usb cord and plugged it back in.. Same issue.. Then I tried to reprogram the start button to another button: It let me reprogram the button as if its working just fine, but it will not let me start the game. I even set the game to freeplay and nothing. Very strange issue. Tomorrow I will see if it effects all the games. I only had time to check Galaga.
Im very frustrated because i let the kids use this arcade all the time and they love playing on it.. but now it has issues. The game will work for a few rounds, then it just won't let you start the game... crazy.