ISA Server 2006 can be used to deny or allow network traffic from or to hosts. Any network application running on a server requires to use a port which can be used to listen traffics coming from the client machines on the same network for that port. Applications configured in this way listen on one or more ports. An application running with two instances is unable to process the requests or fail to initialise properly.
The same case happened with me last night. I was configuring Backup EXEC Agent on a system on which ISA server is also installed. The Media Server which is installed on a different server was not able to connect to the Agent. As you know, Backup EXEC listens on port range - 10000 - 10025. I configured an outbound rule in ISA Server so that Media Server can talk to Agent properly but it wasn't happening at all. I looked at the Task Manager and found that there were two instances of Backup EXEC process running in the Task Manager Process tab. I killed both the processes and then restarted Backup EXEC Agent Service.
The solution for this is described below:
1. Media Server must be configured to use Dynamic Port Range from 10000 - 10025
2. Create Ports and Protocol using ISA Protocol tab in right pane. ISA Server must be configured to allow traffic from ISA to Media Server for the aforementioned Port Range.
3. Firewall Client Installation must be enabled on ISA Server.
4. Kill any duplicate process if it is running in the Process Tab of Task Manager.