iBooks says that books that are on my iPad are "Not on this iPad"

My problem is two separate issues, both with iBooks.

First: My iBooks on my iPad Mini says that books that are in the library are "Not on this iPad". Why and what can I do? They are uploaded and in my iBooks library and iTunes store on my computer says that all my books are in my library.

Second, have 13 books in my iBookstore on the iPad Mini that says is ready to updated, press update all and nothing, press them individually and again, nothing. Seeing the bright red circle with the number in it at the bottom of the library is annoying.

My iPad is up to date with the latest downloads.

Any ideas?