I had a feeling I was experiencing something similar to this. What I found was three albums worth of tracks that had been lost from the playlists. I don't have any extra playlists apart from those created when loading files. i.e. all my refs values should be 1. These showed up as refs == 0. This is probably due to my stuffing around with the fids directories.

Anyway I thought there was supposed to be some sort of Unattached Items playlist where files like this would end up. However I can't seem to find it. It only seems to appear in the Hijack playlist. Is the only way to get to these files by doing an advanced search for refs=0 and the copy and pasting into a new playlist... or simply deleting them and reloading them thus recreating the playlists?