The problem is that epub is the standard for publishing these days, so I don't think Alex is wrong for using Calibre for the conversion, the fact of the matter is there is no perfect conversion tool for epub to mobi. A number of ebook creators that are publishing to Amazon report that Amazon's own Kindlegen is worse in most aspects compared to Calibre, and to get a decent conversion they use Calibre, then Mobiunpack, and then Mobipocket Creator to gen the final pub-ready version.
I've been doing some further digging since my last post - there seem to be some bugs in Calibre's handling of both font-size and vertical-align css handling for <sup> tags (or any tag using vertical-align:top for that matter). Fixing the vertical-align:top conversion was trivial, but need to do some more digging to figure out how to fix the font size.
Last edited by ldolse; 04-12-2011 at 08:23 AM.