Not All iPad PDFs in Various Collections Appear in OS X Maverick iMac iBooks app.

I have a number of PDFs on my iPad categorized into a number of collections. After I upgraded my iMac from Mountain Lion to Maverick, some PDFs from one of my iPad collections ("Manuals") automatically appeared in the iMac iBooks app, but not all. How do I fix this?

Thanks for your reply King_Penguin
Re your first point - 'Sync collections' was ticked in both the iPad and Mac versions of iBooks prior to these problems occurring.
Why have recently purchased or installed books been moved to iCloud and moved off my iPad and iMac when previously they were there in my iBooks library collections? They were books I'd read or were in the process of reading.
More confusing is that on my Mac in iBooks there are books that are fully downloaded and not in iCloud yet the same books in iBooks on the iPad are not downloaded and are in iCloud. After I sync this hasn't changed. To my mind this means that sync isn't working properly or that maybe iCloud has somehow been activated on one device and not on the other?
Why should I have to re-download books that were already present in my iBooks library on Mac and iPad prior to my upgrades to Yosemite, iOS 8 and the iBooks apps?
I have to reiterate that I do not and will not use iCloud and for 2 reasons: it is not secure and Apple uses push marketing to make it difficult for you to not use it.

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Not All iPad PDFs in Various Collections Appear in OS X Maverick iMac iBooks app.

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