This might not be helpful, but the only way I've found to consistently get a TOC in a mobi for Kindle via Calibre is to use Sigil to make an epub first from the source files, then convert that to a mobi via Calibre.
Build the TOC in that using the header tools (basically put <h3> around each chapter instead of using your own inline one. Takes less than 5 minutes.
You can sometimes get it to work the other way, but it seems more like voodoo than anything I can figure out...(mobi just seems to be a weird format to work with).
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