iTunes U showing up in song list
Solution 1:
Changing the "Media Kind" to "iTunes U" under the Options tab of the "Get Info" dialog will move them from the Music section of your library to the "iTunes U" section.
This tends to happen when you import/rip audio files (audiobooks, podcasts, iTunes U, etc.) to iTunes rather than subscribing to them or buying them through the iTunes interface.
Solution 2:
I think this answer may apply to your problem as well.