Your source document is most likely abusing H1 and H2 tags to have bold type on multiple lines. It's more appropriate to use <br/> inside of heading tags to split them across multiple lines - this way the TOC will be able to get the correct data.
There is an xpath under structure detection which inserts page breaks before h1 and h2 tags - remove this and you should be ok, but it means you need to make sure your chapter detection xpath is working correctly.
Alternatively you could try 'renumber chapter headings' under heuristics, but I don't think that will do exactly what you want.
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