So, got the system fully updated, re-compiled 7.2 of the ATI driver for X, and now am experiencing several oddities. The first of which, I seem to lose my mouse cursor when X starts up. Next, some games seem to work just fine while others do not. For example, I can run all of my confirmed working Neo-Geo roms (Double Dragon, Magician Lord, etc) and a select few other games (Street Fighter II) just fine. Others exit immediately with the same problem about XRandR. If you want, I can log on temporarily from the linux box and post some logs.
I forgot to ask, would any of the SDL patches to the ISO have had anything to do with this as well?
[Edit] Ah-HA! It IS in fact SDL being un-patched that is causing my issues. I did an environment variable of SDL_VIDEO_X11_XRANDR=0, and got no issues (but no full-screen switching). So apparently SDL in some way needs additional patching for such low resolutions.