I've found that Kindlegen is pretty "hit or miss" when translating the css from my epubs to the standard in-line html formatting needed for mobi's. I constantly experiment to determine exactly what works and what doesn't, but it's pretty hard to nail down.
Calibre, however, usually does a better job of translating what I intended with my css (I'm sure I get too carried away with my styling). But I want the final product to be generated by Amazon's official tool for ensured compatibility.
My solution? Build an ePub. Convert with Calibre (epub->mobi)... unpack that mobi with MobiUnpack->MobiML2Html... manually create the toc.ncx (and twiddle the opf) and then feed that opf (and html) to Kindlegen. Strip the resulting mobi with MobiStrip. And finally, tweak the metadata with Mobi2Mobi.
It's convoluted, but I've found that my mobi's converted from epubs tend to more accurately retain the original formatting I've worked so hard on.
Last edited by DiapDealer; 03-31-2011 at 12:23 PM.
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