Just a thought - when you talk about removing Calibre, have you also removed its configuration folder as by default this is not removed during an uninstall. It is always possible that there is something strange stored there. Note that if you remove this folder (you could rename it while testing instead of deleting it) you will lose any custom settings you have got set up, and any plugins would need re-installing. After removing/renaming the configuration folder and doing a reinstall you would then need to repoint Calibre at your existing library.
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