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Currently Display Suite hijacks the book navigation field and uses the book navigation block to return the output.
The block module provides separate theming functions, templates and preprocesses for a book navigation inside a node and book navigation inside a block, these are:
For displaying navigation in a block, renders only the table of contents, and uses Render API.
For displaying within a node, prints the table of contents and a book pager with next, previous and top level links.
So Display Suite breaks sites that rely on the book module because the next, previous and top level links are no longer shown on the node page.
Why is this important?
If, for example, http://drupal.org/node/644662 page switched to a display suite layout, the "‹ Devel up Install Display Suite ›" links at the bottom of the page would no longer be shown (and there'd be no clean way of getting them in as the block on the right hand column would have to be overridden as well).
Patch attached that fixes this.