According to Wikipedia http://en.wikipedia.org/wiki/Zip_(file_format) seems that zip files have headers for
File last modification time and File last modification date so any zip file checked into git will appear to git to have changed if the zip is rebuilt from the same content since. And it seems that there is no flag to tell it to not set those headers.
I am resorting to just using tar, it seems to produce the same bytes for the same input if run multiple times.