Try removing the board from the game, and reseating it, time killers if I remeber has 3 boards that interconnect to form the game.
Also, have you checked the voltage yet?
Get as copy of the jamma pinout here ::
http://www.coin.demon.co.uk/jamma.htmGet a digital multimeter.
(Cheap, just look at sears or your local hardware store)
Set it to measure dc, then connect the black lead to ground and the red lead to +5 on the jamma harness right by the board.
If it's low there is a small plastic screw on your power supply that you can turn to adjust the voltage.
The power supply is the small rectangle at the bottom of the case with a screw terminal strip labeled +5 +12 GND, etc.. etc..
DO NOT adjust it without a multimeter. You can take the +5 volts over 7 volts with that and damage your board.
And remember relax, it's just a arcade game, not rocket science.
Later,
dabone