To anyone having the same problem:

Copy your installed lr-fbneo to a new location (through terminal):
sudo cp -p -r -f "/opt/retropie/libretrocores/lr-fbneo" "/opt/retropie/libretrocores/lr-fbneo10"

Edit \\RETROPIE\configs\fba\emulators.cfg
and add to the top of the file:
lr-fbneo10 = "/opt/retropie/emulators/retroarch/bin/retroarch -L /opt/retropie/libretrocores/lr-fbneo10/fbneo_libretro.so --config /opt/retropie/configs/fba/retroarch.cfg %ROM%"
and change your default emulator for Final Burn Alpha in EmulationStation to lr-fbneo10

@sirhenrythe5th I only use shaders for scanlines, specifically the horizontal and vertical zfast-curved shaders. I don't know if those are libretro only. If Adv.Mame has scanlines as well, I am curious to see which I like better ;)

@TheBlueBanner could you try again when running in verbose mode? it's an option in the runcommand when launching