I've set up RetroPie in Raspbian Jessie and am able to start it up. I have a SNES controller and configured it on the first start up. It works perfectly fine in the menu, but when I select a rom, I get a pop up that says USB Gamepad not configured. I'm using version 3.6 of RetroPie. I tried following this link
https://www.youtube.com/watch?v=AhkEnDdygbQ (useful part is at 5:40)
opt/retropie/configs/all/retroarch.cfg file is empty so I'm not sure what to do to make my controller work in games.