I noticed that the command line 'zip' tool and Mac OS X's 'Compress XXX' option (available via right click in finder) are giving different output files. Not only is the size of the file a few hundred bytes bigger but the content is significantly different as well.
How can I find out what command the Finder is using for compression?
The answer is in
man ditto
:Take a look at An AppleScript to compress a Finder selection article.