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It could be that the blank rectangle is the "original" cover that stays there unless removed. In Aldiko, I don't see the new cover that I just added in Calibre as the first page of the book. What I see is the "old" cover, an index or a blank page (whatever that "original" was). There is a plugin that allows the removal of the legacy cover, it's called "Modify ePub". If you run your books through there first before doing your epub to epub conversion, it should clean up your "quirk".
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