If these are podcasts, I had a very recent similar problem with syncing (albeit I was manually transferring) previously OK podcast content to my wife's Nano after upgrading to the latest iTunes. It now just wouldn't drag and drop (or sync), but, oddly it would to my iPod Touch.
To cut a long story short, it appeared to be something about the mp3 tag metadata embedded in the file that was causing problems. I simply changed the filename (in iTunes -- not in the Finder -- select the file, and I added an a to the end of the name) which I'm guessing forced iTunes to rewrite the mp3 tag metadata and that seemed to clear the problem.
I renamed the file back to its original name once it was on the Nano, and all working fine with everything correct.
Could be a similar mp3 tag compatibility issue with your iPhone as well, as worth trying on one file to see if it works. I didn't try but also figured changing the tag info (select a podcast and Cmd+i to bring up the tag info) would also force a data update to the file and solve the problem.
Suggest Apple software look up the meaning of "regression testing".