OK here are two brand new tests, with the exact settings and steps I am using:
Exited Emulationstation and tried the scraper with default settings and it still didnt do anything- it instantly says complete.
I then deleted the gamelists from both folders whilst emulationstation was closed.
Ran the scraper in emulationstation again and this time it outputted a file which I could use. The only difference I did this time was made sure emulationstation was closed when I deleted the files- I thought I had done that before but maybe I hadnt and that was the difference.
Weird that it doesnt work outside of emulationstation just for the SNES and weird that it just worked this time- I had tried for 2hours constantly trying different settings/combinations of trying to do it before. No idea why it worked this time but it worked so I'm happy now!
Thanks for your advice