I am having the same problem, but with an iPod touch (I think the issue is related to an iTunes bug). My iPod touch is set to manually manage music. I'm trying to restore music to it lost from another iTunes bug. Please let me know if you find a fix.
How to delete files in iTunes: http://support.apple.com/kb/HT3842
You can enable many, but not all, of the interface elements from the previous iTunes by selecting the appropriate options in the View menu (such as Show Status Bar, Show Side Bar).
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