well – some games in fba-libretro really dont like select being the hotkey, some games wont accept select as the coin button. So its common to set for fba-libretro, the hotkey to be something else like left trigger for example (you just override it in the fba retroarch.cfg).
This way it seems to improve compatibility.
Out of interest, what does your neogeo.zip for fba look like?
Mine is here (which is based on the dat file):