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Did you look in the registry? The MS Trusted Installer writes stuff there; the uninstall should have cleaned it out, but maybe not in this scenario.
Take a System Checkpoint, install CCleaner if you don't have it and use its Registry Cleaner - you may have to run multiple times to to get a clean sheet. If something goes wrong to do a System Restore.
Rather than installing Calibre from an MSI on a non system drive you might want to consider using Calibre Portable, which is completely self contained.
BR
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