The calibre settings for WhisperSync/covers/etc. have no effect.
Amazon's Personal Documents intake post-processes the ebook to mark it as a PDOC, link it through WhisperSync to the PDOCs section of your Kindle Cloud, and depend on WhisperSync for the cover.
PDOC covers will ONLY download through WhisperSync for a PDOC downloaded as MOBI. That means you must convert to "old" MOBI, not "both" ("both" means newer devices will download the AZW3 portion). At least for the E-Ink devices -- it is possible the Android app works differently, but I have never tried.
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