I am fairly confident I know what causes this. I had the same problem after I updated my iPhone 3GS to iOS 5 in January 2012. Certain media files would not sync and remain greyed out in the drop down list under the device, regardless of whether I synced my entire library or manually managed it. The problem remained even when I bought a new MacBook Air, a new iPhone 4S, updated my iOS software, and updated iTunes. The only constant that remained was the library database itself. Therein lies the problem.
If you read these threads, a lot of people will talk about voice memos, photos, e-books, etc. They'll say "I got rid of an old voice memo and the problem went away!" Someone else will say "I got rid of an old e-book and problem solved!" The corruption is occuring in the library itself or in how iOS is communicating with the library files. I think it's probably the later, as I rebuilt my .itl library file after exporting my library to an .xml file and that didn't fix it. What did resolve the problem was removing from my iPhone all the older music I had added to my itunes library prior to the upgrade to iOS 5. Once I did that, the sync completed without problem. I accomplished this by only syncing checked songs and then removing the check mark from everything that was over a year old.
Much like others with their voice memos and e-books, I believe the problem relates to media files added to your itunes library prior to the upgrade to iOS 5. Which media files are causing the problem varies from user to user. For myself, it was music and not simply one file. Many of my music files seemed to create the error. Thus, I removed them all from my iphone.
The problem will reoccur if u simply delete the media file from the library and then add it back. The library, or how iOS manages the library, seems to retain memory of whatever is corrupting the process. I am content with leaving out my older music at this time, since i've played out most of those songs anyway.
I suspect a permanent solution would be to set up a completely new itunes library. I haven't done that yet, as i'm still hoping Apple will come through with a fix eventually.
But don't bother restoring your phone. It's time consuming and won't fix it.
One caveat -- I never tried an iOS restore and then set up the phone as new, as that was an unacceptable option to me. I didn't want to lose all my previous text, call, and app history. However, deleting old backups, creating new, and restoring from them -- which I did do -- has no effect.
I hope this helps.