When you plug the controller in (or turn it on or whatever), does it flash a notification on the screen saying something like "blah blah gamepad number/number not configured"? If so, you should be able to create an autoconfig profile for it by going to settings > input > port 1 binds and then 'default all', then 'bind all', then 'save autoconfig profile'. Once you complete that process, hit 'default all' again, quit out of RetroArch and then when you come back, it should recognize and autoconfig the pad.