Theres potentially a few issues there (mainly with the way you have used RGUI to save your nes config). I would be sorely tempted to start again with a fresh image.
If you really dont want to, a bodgy way to get your other systems to work the same way would be to copy your nes retroarch file across to them.
Backup before you try this, but it would be along the lines of
sudo cp /opt/retropie/configs/nes/retroarch.cfg /opt/retropie/configs/snes/retroarch.cfg