iBooks books & PDFs not showing/syncing with iTunes

I'm running iBooks 1.5 and iTunes 12.3.3.17 on MacOS 10.11.4 (which should be the latest updates of all software and OS). I've noticed that when I try to load PDFs or Books stored in iBooks onto a device (iPhone6 Plus and iPad2) that many of my Books and all of my PDF files are missing from the iTunes, device sync window. That effectively means that I cannot load PDF or some ePub content onto my devices. Has anyone else noticed a similar problem?

I've got approximately 90 PDF's stored in iBooks but when I search for them in iTunes it's showing zero (see screenshot).

Equally, I've noticed several ePub Books have disappeared, some are in Collections, some are not.

I have not seen this error before (ie; I've always been able to locate PDFs and Books via iTunes to sync to my devices).

Does anyone have any ideas? This is rendering iBooks useless.