Thanks! It looks like that was the problem. When I reboot the problem disappears so I disabled fastboot and it appears to have fixed the problem.
However, is it normal for the games to look very blurry?
Here is Marvel vs Capcom:
I'm using a Radeon HD 6450 with VGA to a Crescendo TC1600 (VGA -> Component) using high quality VGA and component cables to my Toshiba 27A34 CRT.
Also, Arkanoid seems to be using a refresh rate out of spec for my CRT?
SwitchRes: [arkanoid] (1) vertical (224x256@59.185...)->(768x512@58.483753)
I've tried re-running VMMaker and selecting ARCADE_15 (standard) and Generic 15 kHz (and re-created/installed modes/rebooted) but it didn't help.