it's something that will never be perfectly fixed, but it's just how your monitor accepts the information and puts the data on the screen. a normal computer monitor has an automatic centering of the picture at your single resolution that you use, with an arcade monitor, it's got all sorts of resolutions and frequencies, and can only save so much of your data.
the trick i've heard for getting it as close as possible to perfect is to go back to your restool and make it so mame pops up those warning screens and center the white box for each resolution manually using the little menu thing attached to your monitor. of course it'll always be a couple pixels off, but that's better than what you have now. most of the time, you'll only have to move the screen image and make it larger or smaller, since tilt and pincussion stuff should stay constant over each resolution.
get it?
EDIT: this problem has everything to do with yopur monitor and nothing to do with your software. You'd get better answers in the monitor forum.