It seems like closedir is not correctly closing a directory handle.  rmdir will fail if you try it after calling opendir and closedir.  rmdir works fine if you don't call
opendir / closedir.

The problem does not occur in 4.0 or 4.0 pl 2.

<?
   // Run this script twice.  The first time you run it, 
   // you'll get a failure
   // that RmDir failed (Permission denied).  Run it the
   // second time and you
   // can successfully remove the directory.  It seems like 
   // closedir might
   // not be closing the directory.
   $dummyDir = "test";
   if (!is_dir($dummyDir)) {
      mkdir($dummyDir, 0777);
      $handle = opendir($dummyDir);
      closedir($handle);
   }
   rmdir($dummyDir);
?>