Ok this may be the problem (although originally I didn't think so), as I found old playlists that were from two computers back and I can't find the playlists on the last computer. Where should they be located? Here's the file structure:
Music
Amazon MPD
iTunes
Album Artwork
iTunes Media
...
Music [all the music files are in here, and that's working well]
...
...
My Playlists [contains the old old ones]
Playlists [only contains samples that don't show up in iTunes]
So it seems the two existing Playlist folders are not connected to iTunes (as those lists don't show up), but I can't figure out where the playlists that are in iTunes are actually stored.