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I'm glad you got it working, but fwiw, most of my ebooks have a "toc" reference in the <guide> section and they convert fine to MOBI-both and open as AZW3 on my Kindle Voyage, so it doesn't seem like the existence of a "toc" <guide> reference is the only factor.
The only difference I can see between my working "toc" references and your non-working reference is the working references point to a complete html page without a # anchor -- e.g., <reference type="toc" href="text/part0001.html" title="Table Of Contents"/>
Perhaps having the # anchor messes things up??
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