Reply To: Controller setup working fine on menu, but not in game

Can you backup the file
/opt/retropie/configs/all/retroarch-joypads/Twin_USB_Joystick.cfg

then delete it and make sure that directory is empty.
Then run the retropie-setup script and choose the register a retroarch controller option?

That will write a file back to the directory above – can you try that one out (and post the file)?