Phantom files cannot be played, they do not exist. It just skips all the phantom duplicates in the song list (the ones starting with a period and underscore) and the message "skipping unplayable files" appears for a couple of seconds at the bottom of the screen.
Renaming the folder is a good idea, but did not resolve the issue.
None of the folders contain anything except the actual .mp3 files (there are no .m3u or any other file types in any of the folders).
Thanks again for the suggestions, would really like to run this glitch down!