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It is nobody's fault but yours if you try to do what ebooks are fundamentally designed not to do.
calibre will attempt to set the cover in each way it can be specified, which is the best way to make sure it works everywhere.
The Kindle ebook specs say that cover.xhtml is invalid (and it will ignore them if they exist, I suppose, but there is no mobipocket tool in existence AFAIK that will create one) and thus conversions will always remove that in favor of using the metadata cover.jpeg in the appropriate meta field.
You can specify whatever you want in an EPUB, if nothing else then by editing the raw text files -- that still doesn't mean any ereader/app/program will respect it. Especially if it runs counter to the accepted conventions.
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