Rather than start a new thread I figured I'd just bump this one.
So I'm now trying to set up groovymame on a different PC but with the exact same gfx card and all the same files that were on my previous PC, just a new install of windows.
I had the PC connected to a PC monitor running a very high res then started groovymame as normal with ms pacman. Obviously out of the PC monitors range so connected to my cab and it looked fine.
Then I reset the PC with just the cab plugged in and as expected windows detected the low res monitor and displayed it all correctly. However now EVERY game in MAME is just squashed up in the middle!
I tried adjusting the dot clock (though not should why I'd need to) to 8.7, same thing. Then I checked arcade OSD and all resolutions there display normally. So what's going on? Nothing has changed in any of the configs, I just restarted the PC! The desktop resolution changed but why would that affect anything else??
*EDIT* Dodonpachi DaiOuJou is displayed correctly