I think the "problem" here is that the Kindle app will display the cover image specified in the cover <meta> tag when you open a book. With an ePub, you need to specifically include a separate HTML page with the cover in the spine in order for it to appear when you open the book in most readers.
That said, my understanding of [url=http://blog.threepress.org/2009/11/20/best-practices-in-epub-cover-images/]ePub cover best practices[/i] is that you shouldn't be showing the cover when you open the book - tell the reading software how to find the cover, but let it decide whether or not to display it.
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