I only have one reference to each song (i think)>

The playlists are a series of artists > then you can drill down into the albums > then drill down into the songs.

Does that make more than one reference?

I have deleted some songs (below 7400 now which is how many i had when shuffling the entire player worked) and it is still not remembering the place. I "forgets" on restart if there are more than two albums (50 songs or so)