OK Steve, I've been able to recreate part of the problem. Here's the steps:
We're going to make two playlists from the same album, we'll use the first 6 tracks of the album. The track order is important in reproducing. Start w/an empty iPod.
1. Playlist #1 = songs 1,2, & 3 from the album
2. Playlist #2 = songs 4,5,6,1,2 & 3 from the album
3. Sync
4. Change the Album Name (I just added an "A" to the end of it)
5. Sync the same 2 Playlists and check Update Tags
6. Check your iPod. On mine, there are no Playlists at all. Also, doing a Browse>Artist>Albums shows the one Album (correctly updated) but the Album only has the first 3 tracks of Playlist #2 listed (songs 4, 5 & 6). Not 6 songs as you would expect.
I've done this a bunch now and consider that reproducable.
Here's the interesting thing. Viewing the iPod in MC it shows up fine, but looking at the iPod itself shows the missing playlists and tracks on the Albums as listed above.
Now, the track order needs to be the way I listed. If you do it this way:
Playlist #1 = songs 1,2, & 3
Playlist #2 = songs 1,2,3,4,5 & 6
It works fine. More strange, no?
I think you must have some logic messed up somewhere that's causing this problem. Aw, heck. I don't know what I'm talking about. But at least this is reproducable and is probably the root to the "empty" ipod databases that Fex and I have reported.
Here's a copy of my iTunes DB in this corrupted state:
http://www.home.earthlink.net/~ashawley01/data/Hope this helps.
Adam