Only submit files that have changed. Don't save the directory info when zipping the files.
Example: On one of the skins I submitted recently, I had the files:
109E4-1.bmp
109e4.txt
materials.txt
info.txt
and a small zip file with some references, but I note this in my "info.txt" file <-- that's how I do it anyways.
EDIT: Nope, I've had no confirmation emails for a while now. Pyro's on vacation right now, so I hear.