Baron,Did you find a solution? I have a customer with the same problem - ports going out of service for few seconds while callers hear screaching sound or dead air during that time.
Check this:http://www.cisco.com/en/US/customer/docs/voice_ip_comm/unity/5x/troubleshooting/guide/ex/5xcutsg170e.html#wp1049561and also make sure that you have the correct IP Address or the full FQDN in commserver\cscoserv\ciscopca\web.xml under unity...