I used to only run MAME and Daphne, all at the same resolution as MaLa and did not have any problems. However, now I'm running Makaron for NAOMI arcade games and it does not have the option of controlling the output resolution so I sympathize with you.
I made sure to set my desktop refresh rate to the same as the games (assuming the games are running at 60Hz) and still no improvements.
I might have to mess around with the layout to see what I can do.
If anyone has any solutions, I'm all ears as this is rather annoying.
Thanks.