1) This is typically due to the cover being part of the EPUB itself. So the EPUB will have the cover as part of the content and set as an EPUB cover. When converting calibre includes the cover and all content (there is no distinction of what the content actually is).
2) Set the margins to 0 and see what happens. There are some strange things with MOBI and margins and with the Kindle that I can't remember off the top of my head...
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