I have installed the latest build, PHP 5.2.10-dev. Same results.

From phpinfo():
Zip 	enabled
Extension Version 	$Id: php_zip.c,v 1.1.2.50 2009/03/01 17:35:25 iliaa Exp $
Zip version 	1.8.11
Libzip version 	0.9.0 

Updated test script (will output 2, should be 0):

<?php

// create empty file
if (file_put_contents("empty.txt", "") === false) {
  die("Cannot write files");
}

// zip it using ZipArchive
$zip = new ZipArchive();
$zip->open("corrupt.zip", ZIPARCHIVE::CREATE);
$zip->addFile("empty.txt");
$zip->close();

// open the file, show compressed size (returns 2, should be 0)
if (($zip = zip_open("corrupt.zip"))) {
  // read first entry
  $zip_entry = zip_read($zip);
  echo "Compressed Size: " . zip_entry_compressedsize($zip_entry);
  zip_close($zip);
}

?>

RTFM:

"zip_entry_compressedsize()
Returns the compressed size of the specified directory entry."

When you use the correct function zip_entry_filesize() the output is 0 
as it should be. Also the "corrupt.zip" is not corrupt at all, you can 
unzip it just fine with regular unzip found in pretty much every *nix. 
:)

The function zip_entry_compressedsize returns the compressed file size (referred to as "directory entry" in the Manual), which is 2 bytes for a zero-size file. The actual (uncompressed) size returned by zip_entry_filesize indeed is 0, which is correct, but that was not the issue.

The problem is that the bsdtar program has only recently been patched for this issue as can be read here: http://code.google.com/p/libarchive/issues/detail?id=3

If you would have executed the provided code and opened the zip file in any program you would have seen the compressed size is 2 bytes, which is "a silly thing to do, as it only makes the file larger".

We are not always able to patch libarchive/bsdtar, neither are we always able to use other programs than tar.