Run gba emulator and hit F10 for keyboard. A new screen comes. Map joystick. If you restart game and gamepad needs re-mapping then you have to change permissions.
In ssh type:
ls -ld /opt/retropie/emulators/gpsp/raspberrypi
For changes to be saved, the user should be pi, not root. The output when this command is run should be similar to below.
drwxr-xr-x 2 pi pi 4096 Jul 8 14:21 /opt/retropie/emulators/gpsp/raspberrypi
If root is the owner, then change the user to pi with the following command.
sudo chown -R pi:pi /opt/retropie/emulators/gpsp/raspberrypi
Quick question: Have you experiencing any sound appearings and dissapearings?