I've seen the monitor struggle (ie not work) with games that are designed for 25Hz displays. Pretty much every CGA-res game I've tried (1942, pacman, bombjack, SF2, wonderboy) all worked.
I just rang the monitor vendor. They suggested that Mortal Kombat has a setting on the board to select between high, med and low res and maybe this is why I couldn't sync... sounds like BS to me but I thought I'd put the question out there... is there merit to their claim about a res switch? Some seting to flag in MAME?