I just checked before you posted and I am not getting the yellow text on booting up a game as I do on all the other RA emulators, even though the controls work in game and in the RGUI input settings it has the USB,2-axis8-buttongamepad listed as the device type.
Yes, this is a RetroPie 3.0 beta 2 image downloaded from this site.
EDIT: Changed fba RetroArch config text to: # include “/opt/retropie/configs/all/retroarch.cfg” and unfortunately that did not do anything either.
So, we can see that as the yellow text is not appearing on start up it is not finding the gamepad config file that the other RetroArch emulators use. Is it using some other file?
Have we exhausted all possibilities at this stage and should an issue be opened on github for RetroPie Setup or is this an upstream issue?
I wonder how yours is finding the correct gamepad config. These roms are all running on lr-fba using the FB Alpha v0.2.97.30 romset