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Calibre only understands single extensions. The .kepub file is strictly for calibre's internal use. There's two ways you can go about this:
1) Ignore anything on your file system, only use calibre and the extended driver to transfer books.
2) If you need the actual files for any reason (and with what you're doing I can see a number of legitimate reasons) manually add the .epub extension. When you send a book to a Kobo device it must have the .kepub.epub double extension, but when sending to any other ePub reader it can either have the same double extension or only the single .epub extension.
I can't make the calibre converted file have the double extension, calibre doesn't know about double extensions and the effort to make it understand would be significant, highly error-prone, and of questionable value since only this single plugin can even try to make a case for needing it.
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