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I don't see anything in either the html or the css that should cause that, but then again... I don't know the particular quirks of the Nook, either.
Perhaps the Nook has issues with empty 'h' tags? Or self-closing 'a' tags?
I'd start by removing the whole nested, yet ultimately empty h1 monstrosity at the beginning and see if that eliminates the "My Chapter Is One Big Link" issue. If so, add the elements back in one at a time and determine where things go pear-shaped. Better yet; the ncx/toc can be pointed directly to the top of the Chapter 24 file (instead of an anchor/id) and top-margin space above the chapter header can be achieved without all that empty nested structure (if removing it eliminates the problem).
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