When using the WordRMR(a word plugin) to create the LIT file and I also have noticed the same problem. When I expanded the LIT created by WordRMR file I saw there was only one html file and no TOC HTML in the lit file, typically LIT files have 2 or more html files. One is the main eBook text the second is the TOC.. I'm not sure if Calibre uses the additional file to create an external TOC, but I suspect it does.
What would be nice is if CALIBRE could create a TOC from a LIT by searching through the main HTML file.
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