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This is just me, and I no longer use a Kindle but, back when I used my Kindle 3, I always got my ebooks looking and working the way I wanted and then performed the final conversion to mobi with Calibre. I just found the results were much better from Calibre when compared to the results from Kindlegen. Of course, that was just me and that was a couple of years ago. Still, even though I have Nook HD+, my wife has a Kindle Fire HD and she's always had good luck with converting from epub to azw with Calibre. You may want to give it a try and compare the results.
- Byron
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