First of all, the good news. I fixed the double bullet point bug by adjusting the EPUB export menu settings of InDesign. There's an option on the first page of the settings dialog to export bullet lists as styled paragraphs instead of at the default lists option. If it's paragraphs, you get to use whatever bulleted paragraph format you used in your InDesign file. And there's no double bullet points.
Now let's address the issue of Kindlegen stripping out TOCs.
Kovid, thanks for the suggestion. I tried converting to azw3, and the file looks great. The problem then is, however, that Amazon KDP doesn't accept azw3 file uploads. It has to be mobi. So azw3 files aren't of much use to me, although certainly I could distribute them myself instead of mobi.
Eschwartz, as I said, Kindle Previewer and Kindlegen strip out and fail to produce a TOC for any of my InDesign generated EPUB files. This only seems to occur with the InDesign files. Possibly this has to do with that I use the style names h1, h2, h3 etcetera for headers in InDesign.
You can find an example of one of my InDesign EPUBS as the free Creative Comments EPUB version of my novel TURING & BURROUGHS at the book's web page
http://www.rudyrucker.com/turingandburroughs/ If you load this into Kindle Previewer, you'll see that the TOC disappears. But if convert with Calibre, the TOC remains.
In any case, I prefer using Calibre to Kindlegen, as then I have more control over the conversion process. The Kindlegen is a "take it or leave it" conversion tool with no options. Another point here is that I sell my MOBI files directly via E-junkie for my Transreal Books operation,
www.transrealbooks.com