Same problem here. But the problem goes deeper. If I take the original iBook created in Author, add other pages, and even rename and save it as another iBook, there are still issues when I try to put it into my iPad iBook library.
The library doesn't accept the new document despite having a new file name. iBooks just opens the iBook that was already there. The only way around it that I've found is to delete the earlier, similar iBook.
This is a big problem for me. I'd like to be able to keep different versions of a similar iBook available in the library under different file names, say "Draft 01" and "Draft 02."