Different games use different sync rates. When a cabinet is set up the monitor is adjusted for that one game (because most cabs only have one game in it).
Mame breaks that mold. Because it duplicates the original game, it duplicates the sync rate as well. Since this can vary from game to game, one game will not roll, but another game will.
You can force Mame to output at the same sync rate. I forget where it is in mame.ini, but if you do a line-by-line it should jump out.