I had a similar problem trying to execute cgi scripts from the primary ibays cgi-bin!
My workaround was to create a new ibay, with all permissions set all users of my sme box, with dynamic script execution (cgi, php, pl etc.......) and no password!
Drop your files into their respective dirs (html/cgi-bin) and test them!
It may seem lame to do it this way, but atleast I can guarantee that the cgi scripts will execute from this newly created ibays cgi-bin!