After patching Drupal to 6.17 we found that we could no longer log in. Removing $cookie_domain in settings.php fixed the issue, however that broke other things that relied on it, like the upload features of filemanager in FCKEditor.
To resolve the issue, you'll need to set both the $cookie_domain and $base_url variables in settings.php.
$cookie_domain = 'example.com.au';
$base_url = 'http://www.example.com.au';
A couple of things to note: