A simple way to handle the problem of capturing stderr output when using shell-exec under windows is to call ob_start() before the command and ob_end_clean() afterwards, like this:
<?php
ob_start()
$dir = shell_exec('dir B:');
if is_null($dir)
{ // B: does not exist
 // do whatever you want with the stderr output here
}
else
{ // B: exists and $dir holds the directory listing
 // do whatever you want with it here
}
ob_end_clean(); // get rid of the evidence :-)
?>

If B: does not exist then $dir will be Null and the output buffer will have captured the message: 
 'The system cannot find the path specified'. 
(under WinXP, at least). If B: exists then $dir will contain the directory listing and we probably don't care about the output buffer. In any case it needs to be deleted before proceeding.