My newest problem... well one remaining problem really, other than this GroovyMame is brilliant and running on Arch Linux it has become my perfect lag free, smooth scrolling set up.

...is some games, eg. Kung Fu Master, R-Type and Indiana Jones and the Temple of Doom (to name a few) seem to be getting upscaled by the video driver and rendering with a lot of anti-aliasing rather than the solid blocky (integer?) scaling I prefer.

At first I thought it was all horizontal games, but a few like Neo-Geo games are fine.
I'm using an LCD 1600x1200 monitor, and have the monitor set to lcd in the config. Whether it's blocky or blurry, game info always says SwitchRes is using the native resolution.
Any advice on preventing this from happening?
TIA