Ok I have found out what the problem is but I still don't know how to fix it. Basically I dropped the filters/access lists on the firewall for a few seconds, retried my connection to the convertor program on the MDS and it worked first time. Now I have put the filters back up and it has stopped again. Therefore there is a firewall configuration problem but I don't know where it lies. I have the standard 3101 port open on the server and mail is coming in and out no problem but still no joy with the BES applications.
Any new ideas out there?