Doh!
Code:
zip -Xvur Author_Title.epub mimetype *
Yay! The extended file attributes store things like Unix user and group id's. They're really meaningless when zipping and unzipping on different machines, so why not compress all files like this...
The zip command is verbose by default, and -u isn't needed for new files, so you can even make this shorter:
Code:
zip -Xr Author_Title.epub mimetype *