@ virtual_ink, re: repeated cover image in Mobi created by kindlegen from epub.
This is a known issue (see post #4 above). To circumvent it you must edit the epub and (assuming your cover image is displayed in its own .xhtml file named "cover_page.xhtml) remove the "cover_page.xhtml" or its equivalent. Just the xhtml file, not the cover image itself. Delete it from the manifest as well.
Then in the <guide> section of content.opf (or equivalent) be sure that there is a type=cover item whose href= reference points to the cover image itself (e.g. href="Images/cover.jpg" or such).
While you're at it, include a type=text name="Start Reading" guide entry pointing at the place where you want the book to open.
Save the edited epub under a new name, and use it to convert to mobi with kindlegen. That should fix the double cover issue.
Or try calibre. IIRC it handles this one for you. I could be wrong about that though.
And DiapDealer gave you the fair dinkum about the various TOC files. With Kindlegen, you have to supply your own inline toc.xhtml in the epub you're converting.
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