Teensy 3.2 works in Emulation Station but not Retroarch

[tonberryhunter]

Im running a Teensy 3.2 as input for my portable RPI3 system. EmulationStation recognizes it and lets me configure the controls but once I load a rom into Retroarch the controls dont work. A config file for the controller is def made as confirmed via ftp. I also noticed that Teensy is showing up as two controllers in Retroarch. Could this be whats causing the conflict? I have tried updating the Retropie software which made no difference.

 

[pilotplater]

What is the teensy's role in your setup? Set up as a usb joystick?