Books in iBooks, but not syncable via itunes

I have 100s of PDFS and books currently in ibooks, however only less then half of the collection can be seen in itunes. Making it impossible to sync the books to my ipad!
Some are purchase from apple, some are not, however half of both collections are not present in itunes.
I have the lastest software for both mavericks and ibooks.
anyhelp on the matter would be greatiely appreciated,
thanks
mackiesmac

That seems to be the case now with iTunes 11, but in prior versions iTunes would automatically download all new books in iBooks, even ones not purchased in the iBookstore. That's why I developed the workflow I've been using. I'm just now running afoul of the changed behavior in the new version of iTunes.
Michael

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