When the itunes library is on external drives. I don't know why that is so but when I move back to plain vanilla setups the issue fades.
I have an ipod Classic 80GB. Recently I had to do a fatal reboot on my computer, but fortunately had my entire music collection saved to my external drive. Anyway, at the time, I had my entire music collection also on my ipod. Anyway, I do the fatal restore, go my PC back to where it was, install itunes, plug in my ipod, and it tells me that it has to swipe my ipod clean and restore with my current itunes collection(which is the same collection I had prior).
So around mid point of syncing itunes gives me an error that it can't sync the rest of my library. So, I exit out, reboot my computer and itunes and it starts the sync again and it completes it. But I am missing about 2000 songs out of my library and for the life of me I can't get itunes to sync these songs. Also, I can play these songs just fine within itunes.