The default settings will only split on H1 and H2 tags. It won't auto-magically put the chapters in a TOC. For that you need the right xpath.
That's why I told you to change the 'Detect Chapters at(Xpath expression).
Change it from the default to this:
Code:
//*[((name()='h1' or name()='h2') and re:test(., '\d+', 'i')) or @class = 'chapter']
And if you can't figure out Xpath for other files just open the file in Sigil and re-save it after using the pre-process option, you'll automatically get a TOC.
In the future use Calibre's bug reporting system if you have a file that you think doesn't work.