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The problematic full-screen pop-up footnote entry for the Word/Calibe version might indicate that the Calibre epub conversion has created alot of unnecessary space below the footnote text entry on test.
Open the epub up in Sigil(free epub editor) or open it using the Calibre Editor and check for any excess space below the footnote text entry in the epub. If there is any excess space, get rid of it.
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