[@mod: sorry for mentioning a specific ROM site, I thought that it would be okay because I did not post the exact internet address of the site]
If some games do work in GnGEo-Pi then the BIOS file you have and the configuration of GnGeo-Pi is good. The only thing that’s probably wrong is that CrlMame did not convert all ROM’s that you have into something that can actually be used by the GnGeo-Pi version that RetroPie uses. Since I do not know where to upload the ROM’s that I have, and given that it is most definitely forbidden to even discuss this on this forum, I guess that you’ll have to jump through some pretty difficult hoops to get Neo Geo ROM’s from romset 0.138 (see this link for info) then from the internet (torrent?).
The link that I mentioned says that GnGeo-Pi in RetroPie uses romset 0.138, piFBA uses romset 0.114 and that lr-FBA uses romset 0.154. That means that if a ROM works in GnGeo-Pi (in RetroPie) then it wil definitely not work in FBA because they need different romset versions.