First off thanks for the great project.
I had my controller working just fine in Beta 2 then I updated to Beta 4. I did the controller configuration and now my controller is not working.
When doing the joystick setup it sees the button presses and writes the config file to /opt/retropie/configs/all/retroarch-joypads/THTTHTArcadeconsole2PUSBPlayer.cfg
What step am I skipping/missing?