If the flicker you're talking about is occuring on horizotnal lines but not so much on vertical lines, then it's probably just interlace flicker. The only real way around this is by using Beta 10 of crt_emudriver, as this is the last version with the flicker filter. It might even be that the USMA is ---steaming pile of meadow muffin--- at interlaced modes... all of which implies you're running an interlaced mode like 480i for MAME, where the game in your picture wants a 240p mode (224 + 8 blank lines each side, so no vertical scaling).
Did you closely follow the crt_emudriver install/setup guide for the 5000-series and up Radeon cards?
Also, that screenshot, is it showing GroovyMAME or vanilla MAME? GM would normally show two resolution lines - one like your screenshot does, telling you the game's native res, and another telling you what resolution switchres has chosen (i.e. the video mode you're actually running at.)