Hi spookybonus,
To get GroovyMAME working with ArcadeVGA 3000,
1.- Create an empty folder, place GM's executable inside. Launch it from command line, with -cc to create mame.ini. Enter mame.ini and edit as usual to point your roms path etc. Don't touch any other video option (syncrefresh, etc.)
2.- In mame.ini, set 'lock_system_modes 0', 'refresh_dont_care 1' -> these options are to deal with ArcadeVGA peculiarities.
3.- Start lauching games
You may find some vertical games run too slow. Create an individual .ini for them with the 'triplebuffer 1" option inside.