On iBooks for Mac, I just created a new Collection. I dragged two PDF into this new Collection, and left iBooks for Mac open. I then opened IOS 7 iBooks and the new Collection and contents were immediately available there.
Next, I selected a PDF within IOS Adobe Reader and chose to open it in IOS 7 iBooks. I then moved it from the default PDFs folder to my new collection. However, when I reopened iBooks for Mac, the additional PDF did not synchronize via iCloud and update into the new Collection. Not what I expected.
I rebooted phone and OS X with no additional success. This may be a bug between IOS and OS X iBook versions, and their iCloud interface.
Don't have any more practical solution ideas to offer at this point. There have been a substantial number of posts on this issue. No solutions that I saw.
Google search: OS X Mavericks iBooks not updating new collection