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What size are the files?
I have sometimes seen zip files contain tiny metadata files (including books) with the same name as the proper file but in a different folder. Using the calibre option to import all files from the zip file can sometimes mean it tries to load the real book as well as the 'fake' book.
Could that be happening here?
Real Epub's are zip files, so you should be easily able to look inside them for more info.
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