Well this is weird. I did some more testing and I found I was able to get the windows and front end showing only by doing the following:
1. Hook up computer to old crt that has always worked for me.
2. Allow windows to load
3. Switch vga cable to the j-PAC one. SYNC OK is lit.
4. Turn on blast. All is well and works fine in windows, front end, games.
That's the only way it works. If I start with the j-PAC vga connected to the computer and then boot it, SYNC OK turns off when windows loads and screen is blank. If I connect no vga to the computer, boot it and let windows load, then connect the j-PAC vga cable, SYNC OK doesn't light and screen is blank.
I'm confused because clearly the monitor is ok with the resolution as it works perfectly if I switch it from the old crt to the Nanao once it's running.
Edit: just to clarify prior to all this I set the groovymame ini file and the vmmaker ini with the Nanao 2930/31 custom settings and reran vmmaker. I also have since tried setting windows to resolutions other than 480i, such as 240p etc and no matter what they all work with help from the other display and don't work when I just try to boot with jpac wired up to pc.
I will also note I am running crt emu driver from a few years ago, not sure if updating would solve anything or not?