/opt/retropie/roms/snes isn’t the right folder. it shouldn’t even exist!
if memory serves, the /opt/ directories should just be
/opt/retropie/emulators (the actual executable files for the various emulators)
/opt/retropie/configs (the config files for the same)
all roms are transferred to and run from /home/pi/RetroPie/roms – the contents here should match what you see in emulationstation.
Right, I think I may have worked it out then. Whenever I’ve had my USB stick in (and I’ve put files into that /opt/retropie/roms/snes folder) then it’s overwriting important stuff on the Pi. So does it copy over roms automatically? That would explain why they’re appearing twice. I’ll tinker more with it this weekend.
The splashscreen comes up for a set amount of time, while ES and whatever else starts up behind it. After the set amount of time, (or if you’re using a video splashscreen, after the video ends) you’ll see the ES loading screen.