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Kindlegen only uses the ncx file for chapter "jump points" on the progress bar (bumping the joy-pad right or left will jump to the next/previous entry in the ncx).
As st_albert mentioned, you must create your own inline html TOC (marked as a toc in the guide section of the opf) for kindlegen to enable the "go to contents" feature. Kindlegen doesn't make it for you from the ncx.
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