I try to buy everything in ePub first, remove DRM (if needed), and then load them into calibre. Calibre then converts it to Mobi so I can send it on to my Kindle 3 (or stay in ePub if it is to be read on my Kobo). I have not noticed any problems. I just finished two books on my Kindle 3:The Girl Who Kicked a Hornet's Nest; and Crown Conspiracy. Both were purchased on Kobo (ePub)and looked great to me when I read them on the Kindle 3.
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