Odd one - about every other time I sync, all but one of my 23 books I have set to sync with my iPad disappears from the iPad. They are still flagged to sync in iTunes, but I have to sync again to restore them to the iPad.
It's not a deal breaker, but I generally only notice when I go to read a book that has disappeared from the iPad!
Has anyone else seen this issue? It SEEMS to only be with books.