IIRC, the folder name should also not be there. On OS X, I just do:
Code:
cd extracted_book_directory
zip -Xr9D ../filename.epub mimetype * -x .DS_Store
Because the mimetype file is so small (in length), it is always more efficient to store it uncompressed, so in practice, no zip utility should ever compress it. You don't even need to worry about that; just make sure that it is the first file you pass to the zip utility.
BTW, if you want to squeeze an extra few percent from your delivery costs, I highly recommend installing advzip and doing:
Code:
advzip --recompress filename.epub