Currently Being ModeratedNov 3, 2013 1:18 PM (in response to cheeseb)
I'm having exactly the same issue. Upgrading my iMac to Mavericks brought all the custom collections and PDFs across. My brand new MacBook Pro lists the collections but none of the content has synced. I can't see any way to force it either. Hopefully it will be fixed in 10.9.1. I've left feedback via the app.
Currently Being ModeratedNov 20, 2013 7:40 PM (in response to cheeseb)
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.