Purchases not transferred even though synced & backed up?

I sync and backup my iPhone and/or iPad before performing an ios update. Even though I have just performed a sync and backup, I keep getting the warning that not all purchases have been transferred.

One time I went ahead and updated anyway and lost all the articles I had saved to iBooks and there's no way to get them back (now I save all articles to Dropbox). I have also tried the right click "transfer purchases" and still get this warning.

My work around is to sync and backup, disconnect from iTunes then update ios without being connected to iTunes so iTunes doesn't delete more of my stuff.