You must create the inline (html) TOC yourself. Kindlegen doesn't automatically create one from the ncx file. The ncx file is only used for the chapter "jump-points" that can be navigated to by using the left/right arrows (or the joy-pad) on the Kindle.
Section 3.3.1 of the
Kindle Publishing Guidelines explains the details of the "logical" TOC (ncx), while section 3.3.2-7 deals with guidelines for creating the HTML TOC (the one you must create yourself).