Steve/Fan_man:
I've seen this before when we were getting the disappearing songs on the iPod, it was before the .34 build I think. You'd upload songs to the iPod and all would look fine in MC9, but when you went to look on the iPod it was either missing a playlist or missing all tunes..basically it looked like it was empty. Even though looking at the iPod in Windows explorer should that they files were there.
It came down to a corrupted iTunes database, although Steve, I never knew how it got in that state.
Fan_man, perhaps sending Steve a copy of your iTunes DB file would help.
Just make a copy of it, it's on your iPod in the ipod_control\iTunes folders. And it's called iTunesDB.
If I may be so bold as to include Steve's email as well:
It's steve @ jriver.com
Good luck guys, because if this bug is out there we're all probably going to run into it sometime.......
Adam