What exactly are you exporting? My guess is that you may be exporting something other than the book collection. You say "Smart Collections" but a book is its own type of collection with an icon that looks vaguely like a book. Are you sure you saved the book (button at the top of the Book module) ?
Yes, I'm exporting a book collection. The icons do look like little books (with the gutter down the center). My saved books are located within the Smart Collections folder. The books have been saved, although I don't have a "Create Saved Book" button at the top right of the book module. The books are saved from the Book pull-down menu on the upper left side.
Oddly, I do see a "Create Saved Slideshow," "Create Saved Print," and "Create Saved Web Gallery," on the right hand side whenever I select those functions, but I do NOT see a "Create Saved Book" in the same tool bar area on the right. Strange ...
You wouldn't see the Create Saved Book button if you are in a saved book collection. So its absence, and the icon's appearance, tell me you were on the right track.
I saved a book, then right clicked it and chose Export this Collection as a Catalog. In the new catalogue, my book layout was exactly as I expected it. So I am a bit puzzled what you may have done!