If you look at the 'Get info' for calibre in the Applications folder, what does it show for the version? Is it possible that you installed calibre in a non-standard location and are launching that version? If you delete the calibre item from Applications and then re-install calibre by dragging it onto the Applications shortcut seen when you open the .dmg file, does that allow the new version to run?
I am assuming that when you say downloading the new version, you are downloading the .dmg file, opening it and dragging calibre to the Applications shortcut.
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