I am also having a similar problem. You're suppose to remap it by using jstest in terminal. It will allow you to see the number the buttons are assigned to which then you assign to in the snes9x.cfg file. I have gotten to this part but nothing has changed for me. Clicking start will still exit the game for me so it's kind of frustrating. I'm using snes9x since Pisnes won't even run at all.