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It is normal if you import an HTML file for them to end up in a ZIP. This is because an HTML based book normally has other associated files such as styesheets, images, more html files etc and putting them into a ZIP keeps them all together.
If you add none-HTML books that are already inside a ZIP (or RAR) then Calibre will extract them as long as there are no other files in the ZIP. If there are other files then the ZIP is added unchanged.
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