A simple toggle on/off of the sync in the iCloud settings does NOT fix this problem anymore.
Obviously Apple misprogrammed ibooks (or the ibooks sync with the icloud) for the mac during one of the last updates.
ibooks on iOS devices still syncs (collections) with the icloud (and between in each other), ibooks on the Mac doesn't.
Unfortunately not even a complete logout out of your icloud and a re-login does help!
iBooks for the Mac just won't sync to icloud.
BEWARE: Login out of your iCloud account on the Mac has become a time consuming and thrilling ("horrifying") experience in case you turned on documents and desktop folder sync to the icloud.
To completely logout and login again has changed from "done in minutes" into a procedure which can easily take half a days up to several days time.
Trying to log out of your icloud on the mac will initiate a download of all your icloud data onto the harddrive of the mac. And the logout will not be sucessfully as long as this download is not completed. In my case the first attempt to log out resulted in the download getting stuck after 4.96GB. After 7 hours of waiting I cancelled the logout procedure. Which is a thrilling thing to do, as during the download your desktop will be completely emptied from all the documents on it... when cancelling the process the desktop will restore, but how can you know for sure...
Just after the first (failed) try to log out, I tried it again, since I still wanted to fix the ibooks sync problem. I let the download happen over night... and in the morning it seemed to have worked. After 1 1/2 days I had finally sucessfully logged out of my iCloud account. I logged in again and my desktop and documents folder were restored (taking hours after waiting again), BUT ibooks still does not sync...
I do not recommend to anyone to log out of their iCloud account, just for trying to resolve the sync problem of a single application. It not worth the time and most probably won't solve the problem.
In the case of ibooks for the Mac I'm pretty sure Apple messed up the syncing and will have to release an update to fix this.
In general: we would now definitely need an app specific "icloud sync reset button" in each and every app using icloud sync in order to enable us to manually trigger a sync or restore the sync. Login out of the icloud has become such a hassle and is a way oversized procedure just to try to reset the icloud sync of a single app.