I would prefer to debug with a libretro core, so
with
lr-pocketsnes
please switch to that and try it first. then ssh in to retropie (using putty on windows or if on another system another ssh client)
and do
/opt/retropie/emulators/retroarch/bin/retroarch --verbose -L /opt/retropie/libretrocores/lr-pocketsnes/libretro.so --config /opt/retropie/configs/snes/retroarch.cfg ~/RetroPie/roms/snes/SNESROMNAME
putting in your game rom name etc.
and then paste me the outputted text via pastebin.com or similar
Snes emulation does work – so either your roms are bad, or your install is bad. it might be worth re-imaging and trying again too.