Ok.. here we go.
Here's a link to the a test html file that made this thing happen.
Something I noticed too: In the viewer when I first 'open' the newly converted file, it looks.. weird! The font looks strange and small as you can see.
But.. once I scroll the file... the font becomes just fine... but as you can see.. the 'Table of Contents' is still there. I was right to call this 'weirdness'!!
I'm very grateful for the time you're taking with this and hope the file and images will help.