As far as I know, Calibre doesn't create that HTML TOC from the metadata (NCX) TOC. It will only create an HTML TOC if it can identify the chapter/section headings - ideally, these should be coded using H1 or H2 (if they are coded differently, you might have to amend the regex used to identify chapter headings). Calibre will then pick them up and create a TOC based on those headings when converting to MOBI. I double-checked, and Calibre will also add the necessary Guide item in the OPF file to enable the Kindle to provide a link to that HTML TOC in its "Go To..." menu.
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