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Are you using dropbox or other syncing software to keep 2 computers in sync? Maybe you have it set to auto backup with the properties for the Calibre folder set to protect. This happened to me once when merging two computers to the same sync. For some reason the wrong copy of Calibre was kept when syncing. I'm relatively sure my problem was operator error.
I bet it has nothing to do with Calibre, but you could uninstall and delete any instance of Calibre then install new.
Good Luck
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