I'm on the latest OS X, iBooks and iTunes. Have 20+ titles in eBooks, most of them added manually as PDFs or ePubs, only 3 bought from Apple.
Thing is, it used to work perhaps a year ago, when I last paid attention. I still have an old iPad on which I have all the 20+ titles synced correctly. But obviously one of the updates since had broken things.
Tried to google for solutions, only to find people reporting the same problems on Apple Support forums, without answers. Any ideas how could one start to even debug the problem?