What happens if you dont specify the joypad buttons in the system specific retroarch.cfg and instead use the auto controller file in /opt/retropie/configs/all/retroarch-joypads/ ?
If you just put the single SNES usb port in the top left usb port, dos it see both and assign them as player 1 and 2 (indicated by the yellow retroarch writing)?
RetroPie help guides: https://goo.gl/Yfy8kj