Well, the actual commands I use are:
zip -X0 file.epub mimetype
zip -X9Dr file.epub META-INF OEBPS
I left out the -X an -D flags because they were not meaningful for what I was trying to say, and I figured they're not actually needed (they say the zip program not to store additional file attributes and directory entries), maybe the -X flag is needed (I still don't think so)?
Other than that, and ignoring that you said you did not modify the mimetype file, I'd think, as Peter says, there's something like a spurious end-of-line or space character.