iTunes syncing of iBooks has been a bit flakey since the OS X Mavericks update and then new OS X iBooks app.
I eventually got books to sync to my new iPad Air using the try-try-again approach. A combination of opening the iBooks app (on the computer) to make sure books got moved there, completely un-sycing all books in iTunes, and then syncing 'all books' again.
That took a long time. I have a lot of books, both iBook Store and side loaded through iTunes on the computer.
Strangely, the iBooks Store on the iPad still shows all the books available for download, even though they are already available for reading offline.
Sorry not to offer better, step by step advice; but it sounds like you already know the basics of how syncing should work.
Good luck.