Confirm your wiring harness, matches to the pinout for this board. Make sure you don't have a ground running to the coin door, that is supposed to be for button 6, or something of that nature.
I had similar issues with a 19-in-1 board, turned out to be the ground at pin "e"(lower case, opposite pin 27) was causing my issue. Using a fully loaded jamma harness from Bob Roberts, it was wired to his specs on his site, which unfortunately is not universal across all boards. My guess, it's a pin on the edge connector, causing your headache.
http://www.jammaboards.com/store/138-in-1-classic-horizontal-arcade-multigame-jamma-pcb.html