How did you generate that TOC entry? I've haven't seen an epub3 navigation document that used nested ordered and unordered lists though I suppose one could be manually generated. What does your epub3 declare as the navigation document in the content.opf The declaration should look something like:
Code:
<item href="Text/nav.xhtml" id="nav.xhtml" media-type="application/xhtml+xml" properties="nav"/>
I've attached a quick and dirty test file created using Sigil and when I click on a link in the toc.xhtml, the cursor is placed on the <h1> tag line. After generating a nav.xhtml document, the links there also work correctly in Sigil placing the cursor on the <h1> tag line. Using calibre's ebook viewer, the <h1> line shows on the screen but not at the top of the page. After doing some checking, I couldn't find anything in the epub 3.01 spec that requires that link to be placed at the top of the page. A page break before might work--if you can find a system that supports it. About the only reliable answer I've found is to split the text files so the header at the top of it's own file.