@endor read last post. If it is not saving and need to be reconfigured everytime you have a permissions problem. If you do have to redo this everytime then hook up a keyboard, press f4. It should take you to console. Type
sudo chown pi:pi -R /opt/retropie/configs/
If it says something that appears that that failed try it without the -R.
sudo chown pi:pi /opt/retropie/configs/
Then restart the pi. Then you will have to configure the controller one last time.