I wonder whether your understanding of what 'your own TOC' means may be the problem.
I think 'your own TOC' means that if your source document already contains a toc.ncx file (known as an external TOC) it will use it, if "Force TOC" and/or "Structure detection" are not used. epub, mobi and lit (and maybe others) often contain a working toc.ncx.
I'm not sure whether a page at the front of the book containing some hyperlinks to other pages (known as an inline TOC) will convert to a fully working toc.ncx.
I never use inline TOCs myself so perhaps I'm not the best person to answer your question.
What format is your source document?
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