Restored iTunes wants to sync old image of iPhone

My harddrive crashed. Bought a new one and restored from iDrive the last version of my iTunes library (several months old). When I try to sync my iPhone apps, by selecting the Sync Apps check box, the current image of my iPhone applications screens (OS 4.0.2 organized by folders) disappears and iTunes displays the several month old version of my applications (pre OS 4.0.2, no folders). I want iTunes to just refresh my apps on my iPhone and backup the current image. I have succesfully synced my iPhone, with Sync Apps unchecked. That sync appeared to backup the phone, but iTunes still changes to view/image of my applications to the old version when I check Sync Apps.

Even more curious, there's no music on my iPod, but when I look in the files on the iPod, the music is still there. I'm not sure as to what I do next, do I delete the music or no?
Also, music + videos = 40 gb. I'm assuming there's some duplicates somewhere on my iPod?

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