Fine! So these are your settings:
vmmaker.ini: monitor_specs_0 = "15625-16662, 49.50-61.00, 4.120, 4.640, 8.760, 0.060, 0.180, 0.960, 0, 0, 288, 448"
mame.ini: monitor_specs0 15625-16662, 49.50-61.00, 4.120, 4.640, 8.760, 0.060, 0.180, 0.960, 0, 0, 288, 448
Run VMMaker with those settings and restart. Then try GroovyMAME. It doesn't matter if you saved anything, it's going to be rewritten by doing this.
Now, I don't know if modes will be automatically centered (*EDIT* VERTICALLY I mean) or not. If the Sony behaves like a real arcade monitor, they should be centered. This means that once you adjust one of them through service menu, the others will be centered too. Only vertical amplitude should need to be adjusted.
But if it does things different than an arcade monitor, then you may need re-center the modes slightly using your service menu.