Are the books from the iBookstore or books you created using iBooks Author? If the former, please list the book URLs in your reply. If the latter, did you create a new book for each lesson, or copy and update your Lesson 1 book to create lessons 2 and 3?
Since you didn't provide enough details, I will proceed assuming you are having issues with books you created, copying from the first one.
When you copy an iBooks Author file, it also copies the book's unique identifier, so iBooks can't differentiate between the two books. If you create a new book for each lesson and copy the previous text into it, I suspect it will fix your problem. You may also want to try File > Duplicate, as that is supposed to generate a new unique identifier. (This has previously been covered in the iBooks Author discussion forum, but I couldn't find any reference on Apple's support site.)