This question was posted in response to the following article: http://helpx.adobe.com/indesign/using/export-content-epub-cs6.html
This page is NOT helpful because the links are bad and the information is not current. Adobe makes enough profit to hire someone to check these links and update the information.
Thanks for pointing out the broken link. I've updated the link to the Kindle whitepaper.
The Kindle whitepaper is out of date. In particular, it seems that Amazon does not accept Calibre-created.mobi files - .mobi files created by converting from .epub to .mobi in Calibre - and insists on using Kindlegen to create .mobi files. In my experience, however, Calibre does a better job of converting from .epub to .mobi than Kindlegen, and I do not know why .mobi files created by Calibre are unacceptable.