I guess that you need to specifically tag your TOC items (for instance adding toc='toc_level1' atribute to every level 1 entry in the TOC) and let Calibre know about your tags in the TOC section (fill in the XPath for level 1 TOC etc) when converting to MOBI.
In addition, you may also want to check the "Do not add TOC to book" option in the MOBI output section as from your description you already have put it to the desired place in the book yourself.
Last edited by janvanmaar; 12-16-2010 at 02:14 PM.
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