I know it is not a fix to your problem with iTunes specifically, but CopyTransManager is a life saver if you don't like iTunes.
It will turn your iPod management to a more logic "drop to/from it the tunes you like, from/to your HDD". That's as easy as it gets. It was recommended quite a few times on this board, and most people, including me, loved it.

http://www.copytrans.net/copytransmanager.php