I have the same issue. I had synching between my iphone and ipad (collections, pdfs) etc. Then I upgraded my Mac from Snow Leopard to Mavericks.
Once, I figured out some permission issues* iBooks had ALL of my collections, PDFs) Everything was synching! Then, I did WHAT I believe ruined it.
I deleted my old user account *(originally, I had to create a new account, when upgrading on the Mac to get my icloud to work. I kept the old account in case I needed some documents etc. The old account was my first and last name. The new account I made was first, middle initial, last name. Eventually I deleted the old Mac user account because my iTunes library would not let my Sonos application create a library due to old permissions.
After I deleted the old account, I opened ibooks and noticed that all my PDFs were missing: GONE! The weird thing, all the collections (sub categories of pdfs) I had made on my ipad/phone were still there, just not the content.
I have signed out of iClould on the Mac, signed back in, still does not appear as it did when I first upgraded. Very frustrating.
Mac - 10.9.5
iphone 6 - iOS 8
ipad 4 - iOS 8