Another "recommended step" when an app misbehaves is to delete the app and then reinstall it. If you delete the app you will lose the books from the iPad as well, but if they are in your iTunes library, you should be able to sync the content back to the iPad. You can also backup the iPad before you delete the app as a safeguard.
You can also try restoring your iPad to factory settings and then restore from a backup. The only issue with this is that so often the backup itself is where the problem lies so restoring from the backup is not always the answer. I'm not saying that it will NOT work, but I'm saying there is no guarantee that it WILL work if you restore from the backup.
However, if you decide to restore your device, by all means restore from the backup and try it that way first!