It only seems to affect Super Mario Bros., and it seems recent, though I can’t say exactly when I last played it on this build (my Super Famicom Pi). This will continue to work until I reboot the Pi. What’s even weirder is that whatever that controller swap did, will stay in place even if I exit the emulator and go back to EmulationStation, play another game with a different emulator, then go back to Super Mario Bros. Of course I then have to switch back to Player 1 to control Mario. What’s weird is I can start the game by plugging the controller into the Player 2 slot and pressing start. I am running RetroPie 4.3.12 (0481bb0) on a Pi 3 with a Raphnet BRD-4NES4SNES adapter and real SNES controllers. At first I thought it was my controller, but I could get the start button to work in EmulationStation as well as in other NES games. I was testing out some controllers with new membranes in them today and thought I would test with good old Super Mario Bros, except I couldn’t get the game to start.

Super mario bros rom world 0-1