Ipod missing songs after update

I never should have done this but when I updated my itunes recently and left auto-sync on. Plugged my ipod in, itunes takes the next 6 hours trying to update my ipod with 40 gigs of music. It was able to do it, and it shows all songs as being imported successfully when i look at my ipod library plugged in to itunes. However, when I unplug my ipod and use it, I only see one song from each album. Some albums are complete but very few. Also, now I can't restore my ipod when connected to itunes to try to reload all of my music. Any ideas?

All of my songs show up on my computer library and are all playable. I've tried restoring to factory settings and even after doing so, I encounter the same problem.
Update though: when I plug my ipod into my car, it can play all of the songs though I can't see them when scrolling through the ipod library. It seems like they're "hidden".
I never get any errors, just can't see about half of my library.

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