Your monitor is running at a different rate than the game. MK is a great example, it runs at a unusual 54.8 Hz (IIRC), while the default for mame is to run at windows' desktop speed (for LCD's normally 60 Hz).
You can reduce this problem enabling one or two of the following options: switchres, triplebuffer, refreshspeed, waitvsync, or syncrefresh. (I'd try it in the order I mentioned.) Note that these options can change the game speed, mess up the sound, skip screens, repeat screens, or other problems.
The funny thing is that you said you're using a arcade monitor, so you probably already have -switchres already enabled, yes? I wonder what your refresh rate is running at. To see what res mame is running MK at, could you run mame with -verbose enabled, and post the info you get on the commandline?
Note that if you are running the games at the native res, the thousands of games in mame ran at hundreds of different resolutions and refresh rates, and your monitor probably can be turned to a few of the them.