Probably something loose. Reseat the harness. Shinobi's usually live well.
System 16 looks the same as Jamma, but it aint.
That was in that Robotron Cab wasn't it? Has a WG 4900 for a monitor?
Check all the connections to make sure they are tight, fire it up, and then take your hand and tap the board and wait for a second. Do it a couple of times.
I'm not kidding. I'm very serious. If it comes up, you have some loose chips on that board or wires. Then you would take it out and reseat the roms.
Lots of places on the net to find the manual. Mikesarcade.com is one of them.