This really does sound/look like a monitor grounding issue. Three ideas to explore.
1) Have a look how your Segai monitor frame is grounded.
Now this is going to be confusing (it is for me), but your logic or DC ground (this is your video signal ground) should not be connected to FG (full ground, or earth ground). FG is at your mains, DC ground is local to your device.
If your FG is also connected to your DC ground, then this can cause the interference you see.
Many people will say you should connect "exposed" stuff like coin doors, metal control panels, and the monitor frame to FG, and many manufacturers do this. Mostly for safety, in case of a short (although not really needed if the monitor frame is normally completely enclosed in a cab). However, monitor frame is usually also connected to the ground wiring behind the tube, which is then connected to the monitor's DC ground!
So, this is a long way of saying: if there is a wire connecting the monitor frame to FG, try removing it, see if it makes a difference.
2) Make sure your home-made VGA breakout cable has all the available grounds connected (pins 5,6,7,8,10).
In particular, make sure VGA pins 9 (5v), 11&12&15 (monitor ID pins) are not connected to your ground.
Make sure that the VGA shield ground is *not* connected to video grounds. This can cause interference. You may get connectivity between video ground and shield ground when cable is plugged into PC, but don't worry about that.
3) It may also be something not connected the right or expected way for the JAMMA. Are you still using the JPAC for connecting the controls?
Someone had a similar issue here recently, swapping game PCBs in a cab, but I can't find the thread. Anyway, I think they solved it by connecting relevant grounds on the JAMMA harness (or maybe the adapter loom, some games use non-standard harnesses).