This is very odd. After posting my question i read several other posts about the same issue.
After reading your question i thought I may have cloned them. Your right K T that is what I did. Even with a new file name, book title, and inspector settings, it caused the confusion when loading a book.
I am not sure if there is a setting that could be changed to solve this problem. But at least I know to start from scratch each time, and not duplicate a template.
Shame I did it to keep the Glossary in my new book. Any thoughts on copying a Glossary?
Thanks for your help KT
Well this seems to have solved my problem. They must have been duplicates from the file menu in ibooks author, and then renamed before they were saved.
A solution was to take the books, create a new template from each one and continue on. Now when they load they each load off the bookshelf with thier own artwork.
Thanks for the help