Can I get you to send me the problematic Zip (or a sample of the output from a 'safe' directory) at avg [at] grandt.com ?
Or jave a look at the file in either a hex editor or wordpad, it must start with PK and end with null characters (0x00).
Also, I really ought to update the examples, the preferred method for delivering the Zip is 
$zip->setZipFile("ZipExample2.zip");
As this will avoid loading the entire Zip binary into memory.
Finalize is called automatically if the zip isn't already finalized.
Alternatively, if you really need to create archices that large, and they consists of multiple files (such as a large directory structure), I'd like to refer to my ZipStream class: 
phpclasses.org/package/6616