How to report a bug:
http://www.apple.com/feedback/ipod.html
I just posted this at iLounge, figured I'd share what I discovered.
It seems that iTunes will not refresh the playlist folder list properly within the iPod after a re-sync.
For example, let's say you have a playlist folder for every letter of the alphabet. You sync one playlist in the folders for the letters A, C, E and M. The iPod will display them in that order.
Now lets say that you decide to put a playlist in that's in folder F. After you sync, you'll find that the iPod has not placed the F folder between E and M, it has placed it after M.
This behavior seems to apply to playlist within folder. 1st sync a playlist that begins with the letter W in a folder. Eject, then reconnect, and sync a playlist that begins with the letter P from the same folder. The iPod will now display the playlist that begins with the letter P after the one that begins with the letter W.
This behavior does not seems to apply to playlist outside of folders. Those are synced properly and in alphabetical order.
The only way around this seems to be to unselect the affected folders and playlist in the iPod sync page, sync to wipe, then re-sync everything to make sure it gets loaded in the proper order the first time.