The exact same thing has been happening to me. I've searched all over the Internet for an answer to the problem but nothings listed. The problem started when I got my new Iphone 5 and started to sync it on my computer from then on everything just went down hill. Every time I add epub files to itunes and then try to sync it to my ibooks library the files don't show up. I'm using the same method that I always used but nothing seems to work. Sometimes when I try to add a new epub file to my ibooks, ibooks would delete some of my other books. Then it's al whole new struggle to get my old files and the new ones back on ibooks. I really don't know what to do anymore..!!