I got excited then, that would have been simple, but no joy. I've got the VGA out from the PC going to the J-PAC. I'm not using the Blast City VGA cable, video is going through Jamma via the J-PAC. I removed the jumpers from the J-PAC now.
I've had a look at the modelines and they contain all the right resolutions, so that looks right. The problem seems to be that without the 15Khz jumper on, it wont flick to a 15Khz signal properly. Usually the monitor makes a noise when it changes between 15, 24 and 31Khz mode too, and I'm not getting that happen.
Any other suggestions? Thanks for the help everyone.