I'm pretty sure that both the command line unzip and the python scripts use the zlib library, but the Leopard gui unzip does not.
Cygwin, which also uses zlib, also fails.
Windows Vista built-in fails, but 7-Zip succeeds.
Windows XP (on the one file I'm testing) asks for passwords for several files in the archive.
Linux unzip fails, which is no surprise since it also uses zlib, but the gui unzip succeeds (I'm using gnome... I think it's the Nautilus archive manager doing the work. I don't spend much time in the Linux gui.

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I'm guessing that there's either a bug in the zlib library, or more likely (especially since this is a problem on the Windows boxes too), the archiving software used by either the publisher or Adobe or whoever is responsible for the post-encryption zipping.
Has this ever been a problem with epubs downloaded from Window ADE, or is this particular on the Macs? And if so, why would we be getting different files?