ADE might be inforcing the mimetype file first requirement (but it is hard to see why). See
Explode and Implode an ePub?, the 2nd post contains a simple way to do this properly under Windows (once I worked out that "explorer" just means right clicking on a folder). Perhaps WinZip is using non-standard compression, which is again fixed/tested by trying a different Zip program
However, if renaming the file and then renaming it back is enough to cause a problem I am out of ideas.