For the games i had problem with like mortal kombat 1-2-3, Hammerin Harry etc i created for each game a .ini and placed it in the mame\ini folder (for example mame\ini\mk.ini) with those settings only:
monitor custom
crt_range0 15625-16200, 49.50-65.00, 2.000, 4.700, 6.000, 0.064, 0.192,
1.920, 0, 0, 192, 288, 448, 576
By changing the bold values (for my TV it's 1.920) i ve managed to centre the screen correctly.
You are right and i already have done this too, that if you play with the Mame menu sliders (press tab in game and find slider menu) you can completely center the games and those are automatically stored on cfg folder for each game.
-The ony thing now i cant figure out is how to get 320x240p on arcade_osd to work with my hd2400 so that i can display correctly emulators and games like am2r. I have played with the values of dotclock with no success (i have tried 6.5 and 8 values on vmm.ini). Any idea? When i choose lower resolutions from 376x240 i get rolling screen.