I have uploaded epubs to the KDP since January 2012, and I've never had such a problem. They convert just beautifully in my experience. I've never used KindleGen because I never could get it to work on my computer. I do have Kindle Preview installed, and I believe that's pretty much the same thing, but again, I've never used it to convert an epub because I like to get as close to the publishing process as I can, and THEN preview the book.
I build my epubs in Sigil, never in Calibre, though I often use Calibre for the opposite purpose (converting library epubs to mobi so I can read them on my Fire tablet). Calibre-generated CSS just scares me.
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