Just taking a moment to share what I've learned after a walk on the wild side with iTunes Sync. I was having a problem getting my iTunes U videos to sync with my iPad. After a comprehensive search of the web, all of the solutions that I found were commercial (i.e. someone pushing a product).
As a programmer, I found the thought of buying a solution wacky (imagine buying a product to manage another product that changes every year). Instead I kept reading and found that the iTunes Library is a plist file (this is a special kind of XML file used by Apple and installed on MacOS). I thought "aha" this must be the problem and so I found an application (from Apple) called plutil.
NOTE- One purpose of putil (usage: putil -s path\filename.xml) is to check whether the plist files are correctly formatted.
To my utter shock, the iTunes Library.xml file was perfectly fine (note to self, make sure to backup this file). Next I tried examining the related iTunes *.plist files and found that these were also correct. Hmm, then I remembered that iTunes also loads a second application when one logs into the system called iTunesHelper.
After researching a bit more I discovered the purpose of iTunesHelper is to assist in the communication between your device and iTunes (interesting). So being a programmer, I did the obvious thing. I closed iTunes, opened my Activity Monitor (on Windows this is the task manager), found iTunesHelper, and turned it off.
Next I restarted iTunes, verified that iTunesHelper was still off, plugged in my iPad, and crossed my fingers.
Voila!, sync back in action.
The lesson learned is that things designed to enable communication may also disable communication when not working properly.
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