Hi Laura,
I'm chiming in here while my genius plugin co-author is enjoying some family time.
In order to help you troubleshoot the way the plugin works with your theme, we'll actually need to see the issue in action.
If you decide to re-install the plugin, and add a book into the system so we can see how it interacts with your theme, we'll be glad to take a look and do whatever we can to help!
Cheering you on,
Kelli