Disqualifier: I'm not a professional, but ...
This happened to me with mine on an old desktop. I never found the problem but what I did was restore the iPod to new and instead of synching, I treat the pod as a flash drive and manually add and delete as I see fit. This took care of the problem.
After a couple of times, you'll devise your own system and it'll become easier. Mine's only 4GB but I still would get bored if I synched anyway.