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I tried everything that I could find in the forums, and it still wouldn't work.
So I uninstalled it and reinstalled it... works perfectly. Nothing like a good ole fashioned reinstall.
Still don't know what caused the problem though.
please read https://retropie.org.uk/forum/topic/3/read-this-first as instructed when signing up on the forum.
also check https://github.com/retropie/retropie-setup/wiki/First-Installation
(You won't see the rom folders with the sdcard plugged into your PC if that is what you are doing - this is in the documentation)