Sync iBooks

What do you mean by 'enabled auto sync' ? The Settings > iBooks > Sync Collections settings on a device doesn't copy books and/or PDFs between devices, all it does is if you have a book/PDF on multiple devices/computers and you move it into a collection on one of them, then it will be moved into the same collection on the other devices/computers - but you have to download (if it's an ibook) or sync (epubs/PDFs) it onto each device that you want it on.

Do you mean that aren't showing in the cloud for redownloading on them ? PDFs (and epub books from other stores/sites) will not be copied between devices and/or iOS devices through iCloud, if you want them on your Mac then you will need to connect your iPad to your Mac's iTunes and do File > Devices > Transfer Purchases to copy them over to it, and then File > Move Books From iTunes in your Mac's iBooks app. You can then sync them to your phone.

For ibooks from the iBookstore, you might be able to redownload them on your Mac's iBooks app via the Purchased link under Quick Links on the right-hand side of the iBookstore homepage, and (if they are compatible with iPhones) via the Purchased tab in the iBooks app on your phone.

Yippie. Apple upgraded iBooks on all devices to sync through iCloud. For the first time all my devices have all my books, whether purchased from iBooks store or not. Great job Apple.