I got this fixed, just in case anyone has a similar issue, I'll post what worked.
It was the video ground. Apparently a Sega New Astro City cabinet uses a separate video ground.
So what I did was this:
Printed out a JAMMA pinout. Looked at the PCB. Both PCB's I referenced earlier looked like the traces from video ground and each set of grounds on the ends of the JAMMA connector met up, meaning (at least to me) the grounds should touch.
I took out my multimeter, set it on continuity, found out that the JAMMA connector in the cabinet did NOT have continuity between the video ground and the cabinet ground.
So, what I did, not sure if this is correct or if I just shortened the life of my monitor... but... I made a small jumper that went between video ground wire and cabinet/common ground. Just a short piece of wire between #27 and #14 on the Parts side of the JAMMA wiring in the cabinet. It worked.
Anyone have any thoughts if this is the correct or a good way of doing this? I could have made a fingerboard adapter, but it I needed a quick fix, no fingerboards on hand.