Well, I don't have an iPod, but here goes. How are you making the playlists? When you make one, aren't you referring to tracks on your hard disk? If so, I don't see any way that the iPod would know what you're talking about once you load it the player, since the directory structure has been lost. I'm sure it just keeps track of which track is which when you upload the playlists by uploading the songs as well. I think that's kinda dumb, but hey, some people here like the soup mode...
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Matt