So. 2 years later and I finally got access to my cab for a couple of days.
Cal you're a genius. I used atom15 to flash the bios and it worked but the same issue I was having before was still there. Now also in dos
The vsync just refuses to hold on any resolutions above a certain size (pretty sure all the interlaced ones)
I removed all the jumpers from the jpac but that made zero difference. Whatever the jpac does to the signal is the culprit.
So I was left with no choice but to wire the monitor direct from the graphics card using the spliced in vga cable I had used back when I had an arcadevga card. As suspected I couldn't do this without cutting power to the jpac or causing it to mix with the signal coming out of the jpac (my jamma connector is soldered to the wires so I can't just disconnect the video pins) so the easiest fix was to just remove the jpac and put my old ipac back in. Luckily I'd left the ribbon cable I had spliced into the controls attached.
So now I have the ipac handling the inputs and a direct connection for the vga output coming from my ati 4xxx with atom15 and cals drivers which covers all cases
Sweet.
Cheers everyone!!
Pod
P.s I have res issues with vertical games. I'll create a new thread about that later
P.s.s I'll never know if the jpac was faulty or my monitor was just picky I guess. I could send it to someone who wanted to try it but I suspect that's more trouble than it's worth.