iTunes sees most iBooks as audiobooks

Most of my iBooks show up in iTunes as audiobooks and cannot be synced as books or read on my iOS devices. They can be synced as audiobooks but I cannot read them. In the OS X iBooks app they all show up as books and can be read.

All of the books with this issue are not from the iBooks store but they are epub files that have been in my library for a long time and have synced to my iPhone and iPad as books without issue in the past.

I am running iOS 8.4.1 on an iPhone 5 and iPad 2, Yosemite 10.10.5 and iTunes 12.2.2 on 2014 13" retina macbook pro.

How can I get back to reading those books on my iOS devices?