Q: iBooks syncing some, but not all, ePub books

I have a fairly large collection of ePub files in iBooks on my computer (10.11.5), many of them from the Baen Free Library, others from sources like Project Gutenberg. I have these books divided into various collections. On my computer everything looks as it should and I see all of the books I expect to see. On my iPhone (9.3.2) this is not the case. I see many of my books, but I do not see all of them. Some, inexplicably and at random, are just not there.

I know that my syncing is working at least a little bit because when I delete a book on my computer it disappears almost immediately from my iPhone (within seconds, at most). Just to be certain, though, here are the settings I have in place on both devices:

Can anyone give me any thoughts on what might be happening here and how to fix it? I'd really like for both my devices to be in agreement with one another. Thanks.