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One issue I have on Kindle when reading books converted from epub is that the character encoding is sometimes wrong, and therefore quotes and other punctuation shows as euro signs and accented letters. When this happens I open the epub in Sigil and save it again (to add a locale or encoding) and then run it through Amazon's kindlegen again. This usually happens with commercial epubs. I've never had a problem with one from the awesome volunteers of Mobileread.

Another one I have is sometimes the Kindle uses the wrong font throughout, and won't change the displayed font no matter which one you choose from the menu. This could also be fixed by editing the epub (IIRC it happens when a font is specified in the boy tag) but I usually just read such books on my Sony instead.

As far as Kobo goes, I don't remember running into problems converting in the other direction, except that maybe with some embedded fonts you couldn't use the advanced formatting options.