Do you use this for anything other than gaming?
If it's only for games, then use a front-end, and have mame32 orient the games vertically.
You mention thats not a set-up you be happy with, why? Only if you are using the PC for more than games.
I'm running Atomic FE with Mame32, games set through Mame32 to run correct orientation with 75% vertical scanlines. I never see the desktop, nor do i have a need at this point. It's a dedicated cab, and Atomic loads when I boot up - running Pac-Man.
Food for thought at any rate.