Forget the Sigil vs calibre stuff, I'll edit some of my previous posts to avoid any more confusion.
I've just had another look at the toc.ncx file inside the source epub. It doesn't look right.
This is an extract:
Code:
<navMap>
<navPoint id="navPoint-1" playOrder="1">
<navLabel>
<text>PROLOGUE</text>
</navLabel>
<content src="Text/part1.xhtml"/>
</navPoint>
<navPoint id="navPoint-2" playOrder="2">
<navLabel>
<text></text>
</navLabel>
<content src="Text/part2.xhtml"/>
<navPoint id="navPoint-3" playOrder="3">
<navLabel>
<text>CHAPTER ONE</text>
</navLabel>
<content src="Text/part2.xhtml#heading_id_3"/>
</navPoint>
</navPoint>
The Prologue entry looks OK. The Chapter One entry is kind-of doubled up. So are many of the other chapters.
If this is tidied up in the source epub, the conversion to mobi should work work OK. I tidied it up by removing the
red bits as indicated, for all chapters. However, not everyone would know how to do this nor would they want to.
The conversion settings in post #14 should correct the toc.ncx by recreating from scratch, without having to do manual surgery.
To avoid this problem in the future, one would need to know how the source toc.ncx file got messed up in the first place.