I’m having the exact same issue. I was initially excited that Retropie included support for my Xbox 360 controller — but after following hours of advice, it is clear that by “support” the developers only intend the Xbox 360 controller to work with emulationstation and Input Control. Using your controller to click through Input Control is fun and everything, but I had assumed that the claims about “Xbox 360 Support” applied to the games (not just to controlling the menuning system). I feel duped!