Thanks for posting, had the same problem/question. Am using Mame32 at the moment and found that 3 settings seem to effect this, turning hardware stretch on/off is the biggee, the zoom control (1x vs. 2x) and turning 3d direct draw off worked on one game. But, pain to do that to load individual games!
I've download commandline mame and a front end to play with. do you have to change just one ".ini" file with the -r switch? or do you have to change a file for each individual rom?
thanks,