IBooks sync works on one Mac, not on other

On my iPhone and iPad, my iBooks setup includes some custom collections containing PDF files. After installing Mavericks on my Mac Pro, the Mac version of iBooks immediately acquired all of the custom collections, and they were filled with the correct PDFs. But on my MacBook Pro, the custom collections showed up but none of the PDF content appeared. I can't find any way to force iBooks on the MacBook Pro to sync.
Any ideas? Similar experiences?

I have an even more unique situation.
When iBooks was part of iTunes, I cleverly used the "Genre" popup within the Info panel for each PDF document to create a "category", e.g. Technical Documents, Proposals, Project Names, etc.
In other words, I treated each PDF like I would a song, and created my own categories (rather than an actual genre like Jazz, Rock, etc.), which I could then sort. As a result, in the iPad, my documents were automatically sorted when using the Categories tab. This works great in all the versions of iOS.
Now that iBooks has been separated out as a separate desktop app, I can no longer sync up these files in the same manner.
It seems that I am now forced to create "Collections" for each of these previously created genres!
As a final note, make sure you have the "Sync Collections" switch turned ON in Settings > iBooks on your iPhone or  iPad, which will ensure that all your Collections sync up on all devices.

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