Could the fact that it's not grounded toanything else be my issue. The manual says if using disk drive type power supply that the ground is already linked. seems a little misleading since it says you MUST link all the grounds and then in the next sentence it says is using a pc power supply not to worry about it.
In my configuration, I use the power in the JAMMA harness to drive the controller board and use a PC power supply to drive the switch boards. I clipped the floppy connector from the PC power supply and ran a write from the ground to the ground spot on the controller board. Voila, common grounds.
While I know next to nothing about fighters, I think that you'll need the main power supply from your cabinet anyway since I believe you'll need -5v for the sound on at least some of the MK boards (IIRC, you can get the -5V to the switch boards using the auxiliary power pins on the switch boards).
So, I guess if I have a question here it would be: is the main cabinet power supply still connected to the JAMMA harness ?
After that I would ask if the LED on the controller board is lit ? What about on the switch board ?
Cheers.