If you mean that it doesn't show up when you click the TOC access button in KPreviewer, but is otherwise visible in the actual book, then that's because in order for a Mobi file to be able to redirect the reader to the HTML TOC via the menus, you have to put a line in the OPF telling the conversion software about it.
Details are in the
Amazon Kindle Publishing Guidelines pdf on pg 12 of version 1.9.
Basically, you just add a <reference type="toc" title="Table of Contents" href="#yourtoclinkhere.html" /> line to the <guide> section.
Hope this helps, and welcome to MobileRead!