I have seen epub files (from commercial publishers!) with zero permissions - you can't even read them... obviously a problem. Unzip the file into a new folder and then check the file permissions.
Also, zip may try to include extra directory attributes unless you tell it not to. Here is what I use to zip up and epub file:
Quote:
zip book-file.epub -DX0 mimetype
zip book-file.epub -rDX9 *
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The D option tells zip to leave out any extra directory attributes.