I think Silver is right on. Refresh rate, resolution and color depth can vastily affect any game. Most will play fine no matter what you choose, just because your proccessor can pump out the power. But some games really dont like it.
Case in point: I like compiling my own mames (to add a couple neo geo games, but thats something else

). My desktop machine is an XP 2500 and the one inside the arcade is an XP 1700. Now both were running the same mame version with the same mame roms, but the 2500 couldnt play Mortal Kombat 3 while the 1700 could. "What gives?" was what I thought. For the longest time I couldnt figure it out. Then I realized that it was the color depth; using a TV defaults the color depth to 16 and using a monitor it was 32. Since both the "switch resolution to fit" and "switch color depth to fit" were unchecked MK3 couldnt change to the optimal settings to match the original.
Anyway, so try those setting and see if they help at all. For reference, im using
mame32 plus.