I'm having the same problem! I spoke to an apple Genius and he said some song would have an exclamation mark next to them. That means the song has been moved from its original location. If you click the exclamation mark it will find the tracks and re sync them.
What I didn't ask was what if there wasn't any exclamation marks next to the tracks!
Find the track (the actual file) and keep it on your desktop or something. Then remove the song with the exclamation from your library, then drag and drop the track from your desktop into itunes again. It should be fine now. This happens when the Song has be moved from its location. I store the music in iTunes only and delete any other files. That way it has only 1 path. To backup just drag and drop the files from iTunes to your hard drive.