I was having the same problem with iTunes 11.4. After doing a search, I found that iBooks is now a separate app that you can open and manage your books from there. Here's more information: Frequently asked questions about iBooks.
Here's the important info that will hopefully help you:
Yes, you can download EPUB and PDF files on your Mac or PC. To add them to your iTunes library, choose File > Add to Library, or drag the EPUB or PDF file to the Books library on your computer. If you're using OS X Mavericks or later, you can add them to your library in iBooks. To read your books, sync them to your device. The books must be in one of the above supported formats.
Long story short: add your book(s) to the iBooks app. Once uploaded in, go back to iTunes, click on your device, then head to the Books tab. You'll see that your newly uploaded books are now up. Choose which books you want to upload to your device and hit Sync. The books should now be on your device.... after such a confusing process. I hope iTunes fixes this in their next update. It's such unnecessary steps just to get books on a device.
Hope this helps!