I managed to get my uploads to work by doing the following -
I found this file - include_phpuploader.php (Directory - cuteeditor_files\Dialogs\phpuploader\)
Then I editid it to modify the following -
/// The global type of upload method to use.
/// Auto|IFrame|Flash|Silverlight
public $UploadType="Auto";
I changed from $UploadType="Auto";
to $UploadType="Flash"; and it's working!