The following is just a guess....
I notice some books have a separate file for the cover (usually a jpeg image). Others seem to have a cover image contained in the book file itself. The ones that have it contained within the actual book file are the ones that open up to a cover image. Most of the time the image is not full screen, but half or three-quarters screen. Like I said, just a guess. I was hoping someone else might chime in with their experiences.....
By the way.... I know you have a large library.
When you update iBooks to the latest version it will take a while for it to index your library the first time you start it after the update.While it is doing that your bookshelf will be empty! Don't freak out, your books will appear when it is done