This may not be the solution you are looking for but I hope you don't mind me contributing.

I had a lot of trouble using my iPod when I first moved to Ubuntu over three years ago. Between them Banshee and Rhythmbox wiped all my covers or wiped all my songs. This was three years ago so they may be better now.

Since then I've been using Virtualbox with Windows XP and iTunes.

This is the only thing I have to go to XP for. I absolutely hate iTunes but use it solely to manage my iPod.