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Check out your files in another product. You might try Sigil - the epub editor, to see if it can make fixing the files easier. Or failing that, try 7zip or similar product (if necessary rename to give a .zip file extension), to make sure the problem lies in the file and not the program reading them. (There are some explicit requirements for zipping into an epub, it's possible the software used to generate your problem files failed to comply and so causing difficulties for software that expects epub OCF compliance. A more generic .zip file utility program may be able to recover the contents where Calibre fails.)
I've never had problems with corrupt zip files (especially in comparison to other compression formats) that could not be explained by file-transfer problems (and the last of those I had were years ago - touch wood).
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