Two-thirds of .pdfs don't appear in iBooks after iPad sync

I'm using a 2-month old iPad 3 hooked up to a MacBookPro.
When I sync, using the Lightning-to-USB cable, I can see 34 .pdf files in my iPad, as its displayed in iTunes on the MBP screen.
Yet, on the iPad, only 10 .pdf files appear on the bookshelves.
As it happens, these are the 10 most recent purchases/downloads. (None via the iTunes Store, btw - books bought at the Store appear as they should.)
I have powered down, done a hard reboot, re-installed iBooks in the iPad, checked that the appropriate checkboxes have been selected under the PDFs tab in iTunes, and toggled between Collections on the iPad. All updates are up-to-date.
I also have iCloud on, but the .pdfs are backed up to the MBP, not to iCloud.
This is a recent problem - previously everything was as it should be.
Any suggestions or thoughts would be gratefully received.
Thanks
Chris Gibbons

The best and simplest workaround for this is to upload the epub/pdf to dropbox on your mac, then open them in dropbox on your ipad/iphone.
I have the first ipad running iOS 5, and this method worked.

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What are the other solutions that you've tried ? As you don't say what you've tried I don't know whether you've done the following or not.
ebooks and/or PDFs that you've added to the iBooks app on your Mac will not show on your iPad unless you sync them to it, only ibooks bought from the iBookstore will potentially show in the cloud in the iBooks app on your iPad for redownloading on it. If not all of your ibook purchases are showing in your Mac's iTunes or iBooks apps (I'm assuming that you have Mavericks or Yosemite on your Mac) then try logging out and back into your account on it and see if they then show.
If you are using the 'sync collections' setting in Settings > iBooks on your iPad and in the iBooks app on your Mac then that does not copy books and/or PDFs between devices/computers, all it does is if you put a book/PDF into a collection on, say, your iPad, then if it is also in your Mac's iBooks app then it will be moved into the same collection on that - but if a book or PDF is not already on it then it won't copy it onto it.
If you want the PDFs (and/or epubs) that are in your iPad's iBooks app to also be on your Mac then you need to connect the iPad to your Mac's iTunes, do File > Devices > Transfer Purchases to copy them over to your Mac's iTunes, and then in the iBooks app on your Mac do File > Move Books From iTunes to move them into it.
Similarly to get PDFs and/or epubs from your Mac to your iPad, connect the iPad to your Mac, select it in your Mac's iTunes, and use its Books tab to select and sync the books/epubs that you want in its iBooks app.

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