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Are those un-named TOC items actually chapters?
It would help if we could see the html code from a single chapter heading. The easiest way to grab that is to use the 'Search and Replace' feature. Click the little magic wand button and scroll through the html code until you see the first chapter and just copy a few lines - the heading and a couple lines around it.
You can also try the 'markup chapter headings' in Heuristics, but based on what you're seeing I'm not sure if it would work.
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