Force iBooks on iOS to sync with iCloud
I've found that if I want to ADD a book, then it's best to add it on my Mac. Then wait until it uploads to iCloud, then after about a minute it will appear in iBooks on my iPhone. I then hit the iCloud icon next to the book title to download it.

If I want to delete a book, then I delete it from my iPhone rather than my Mac. It will then walk you through a few options, until you reach the point where you say that you want to delete the book from ALL iCloud devices. Then it will also delete it from your Mac, after about a minute.