Another thing to do to make sure BD imports as you expect...
1. Check the default settings
2. Check that Book Cleaner is using your input and output files
3. Check that the directory you chose for your BD files is still set as you want if not using the default (under the Sony LRF dialog)
5. Load in your book to edit
6. Edit as needed
4. After editing the book and getting it ready, check your settings in the Sony Reader dialog
I've noticed that sometimes BD loses it's settings. So it's safer to just double check that everything is correct. Otherwise you could spend however long on editing your book only to end up having to start over as your settings are wrong.