It doesn't work for me also. I can (more or less) sync content downloaded from Apple, but not a pdf from my mac added to my ibook collection.
At iTunes, the books tab appeared only once, telling that the books were moved to another app, "iBook".
I also noticed other problems with the sync:
- new collections are instantly listed in all devices, but without the content added to them (just the book that started the new collection).
- not all books are syncronized. I'm just starting to make serious use of this, I have a try with 22 books in my iphone, but just 16 in my mac with several not matching, besides the pdf mentioned above (not purchased in ibook).
Regarding the books not in sync, maybe the issue could be that some of them could have been downloaded with a different appleID? If so, how can I know for a book the AppleID which is linked with?