I have the same problem. I have a nice-looking EPUB that I exported from Indesign 6. At least it looks nice in the Firefox EpubReader plug-in.
But when I use Calibre to convert it to MOBI, my bullet point symbols were doubled. And the two consecutive bullet dots weren't quite the same size, ugh. And the margins didn't look quite like I wanted.
So I tried loading the EPUB into Kindle Previewer and then saving off the MOBI created by that.
So, fine, the double bullet points are gone. BUT my Table of Contents has been stripped out.
(By the way, exactly the same thing happens if I try and upload the EPUB directly to KDP...I think they're using hte same KindleGen that underlies Kindle Previewer. Double bullets are gone, margins maybe nicer, but no more TOC.)
So then I tried loading the Kindle-Previewer-made MOBI into Calibre and converting it to MOBI with a setting to autogenerate a TOC from my headers styles h1 and h2.
Good news, the TOC is back. Bad news, so are the double bullet point symbols. Good news, at least now the pairs of consecutive bullet dots are the same size. More good news, the nice Kindle-Previewer handling of the margins is intact. I guess I'll just live with this fix.
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