Hi Quaristice,
If you are able to get your modes centered by using ArcadeOSD, you need to manage to translate those timings into custom crt_range lines, which will be use by GroovyMAME to achieve similar results. GroovyMAME won't pick the modes you just adjusted with ArcadeOSD. In other words, you need to tell GroovyMAME the "rules" you had to apply in order to get those modes centered, and that's codified by the horizontal porch values you can get from ArcadeOSD. This process has been explained in dozens of threads, so you'll find plenty of information in this subforum.
You may find that getting low horizontal resolution games centered is way more difficult than with higher resolutions. My advice is to always use a dotclock_min value of 8.0 in mame.ini (and possibly in vmmaker.ini too, but that will compromise other emulators). This way low resolution modes will be scaled on the horizontal, allowing for much finer centering.