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I have a more dynamite approach. First, if there are any html-based toc files in the text area, I delete them--never use them on my Kobo. Then I go into the toc editor and empty it completely. Finally I rebuild the toc "from files", and maybe rename a few entries if they are not appropriate, usually front matter files. This rebuilds the ncx with "top of file" pointers and the Kobo loves it. (If there is an epub3 nav.html file, delete that and let it rebuild as well.)
The kind of book you describe almost always has chapters properly in files, so this works about as stated. If the chapters/files aren't properly done, or if there are other problems, that can take a while to correct, but I still find it the best way for reading.
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