We have found the resolution for this. It was an issue with the integration of the SecureClient and the Avaya IP Softphone. With the latest build of the SecureClient from Checkpoint desktop_53717_1_w2k, which is the tech support build 53717_1 of Secureremote client for NG. With this SecureClient version we have had complete success with Avaya IP Softphone via VPN. Another thing to ensure is allow all services on the IP address of the CLAN and Medpro of the PBX, this will ensure that the firewall is not blocking access to and from these ports.
Let me know if this helps you out.