The fact you asked a question in the gngeo-gui thread (issue after use of a usb joystick) and you never answered my counter question, made me not really eager to answer you question here... but let's make a second attempt

What does the rom_path say in /home/user/.config/fba/capex.cfg ?
As you could read in some post earlier, it can be set with a default value of 265104. If so, replace it with the full path to your roms.