@Prusr: I had a similar problem when setting up my Retropie. If you have multiple controllers, the problem lies in that when you copied the controller configuration from controller 1 over to controller 2, you may have changed everything from Player1 to Player2 but at the top of that configuration it says something like “input_player1_joypad_index = 0″. For player 2, you need to change it to input_player2_joypad_index = 1”. I changed the player1 to player2 but forgot to change that and had the same problem. Change the joypad_index and everything works fine.
@ckarini: did you try to follow the same steps for adding the controllers that are posted here? I did that and everything worked fine. The only problem I had was on getting my controller config to work after using the utility. The problem was I needed to direct the output to my proper retroarch.cfg file. Can’t remember the command off the top of my head but was something like “retroarch-joyconfig >> /home/pi/RetroPie/configs/all/retroarch.cfg”. That got my controllers working properly. As for what’s in rc.local, I used the string that was posted here by petrockblock.