Here's a new one:

So with the latest version of iBooks, the iBooks textbooks we are creating are acting incredibly strange. Essentially, when a textbook is opened, the "Cover Graphic" that is displayed is that of a completely different textbook. However, the content of the book is the one that you have selected. Furthermore, when you close the book to go back to the library - by tapping the library icon at the top - the textbook closes with a different "Cover Graphic" from another collection.

This has never happened to us before and can be replicated on all generations of iPad (although we have yet to test it on the iPad mini).

Has anyone encountered or been able to replicate this issue? The iBooks we are using is the latest version and we are also using iBooks textbooks that we have created with the latest version of iBooks Author. We believe that the issue is isolated to iBooks being the culprit, but we are open to suggestions. It is frustrating for us as our students are international and English is not thier first language. This wacky glitch in the UI makes our learning system seem clumsy and confusing.

Any help or suggestions would be greatly appreciated. I've also posted this same question on the apple forums too - I'll let everyone know when things get updated (if they get updated).