When I convert from the epub to mobi, it does not fix all of the formatting issues -- at least within the Calibre viewer. One thing that did improve the formatting in the Calibre window was to convert the HTML to MOBI using the Sony eReader output profile rather than the Kindle output profile. Still, I don't know how this will appear in Kindle. So far, all the mobi ebooks on my blog have been created using the Kindle output profile. Would someone with a Kindle be so good as to download a couple of the mobi books from my blog and tell me how they view?
http://calvinistcafe.blogspot.com/
Thanks!