The .kindle.epub tend to have a mass of media queries in the CSS to allow Amazon to do a better job of converting to KF8/mobi and rather often multiple copies of images in high and low res. They are not readable by a Kindle ereader or app. If you are reading on a Kindle app or device and using Send to Kindle or similar, the .kindle.epub would be a better choice. Otherwise, just use the standard epub.
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