I am having this same issue.
I have been using iTunes for music management for years. I have been using iPods for years. I have never come up with one negative thing to say about it.
I actually made my first purchase on iTunes the other day. I bought season one of Metalocalypse. I would have normally just used a torrent, but I didn’t have time to look then convert files and all that.
Everything was super easy. I had all the episodes to keep me entertained. A few days later, I went to rewatch some episodes and I’m missing 5 of the 20 on my iPod. They are still on my computer, but not on my iPod.
I have the latest version of iTunes which is 7.7. I have the 2.0 software on my iPod. The iPod is the 32 gb Touch.