NAT ports

Hello, I work as the “computer guy” at a small home health agency in Louisiana. We have network administrators who work remotely on our system, and for the past two weeks, we have been having trouble with the firewall, a SOHO watchguard. The network guy has been working with SOHO, and they said that programs like Morpheus, and Gnucleus open all of these ports, making outbound traffic impossible. I have uninstalled these programs from all systems, but the NAT ports keep opening. Is there some other program that opens these NAT ports. It is really frustrating, with the network guys being out of town, and hard to reach. Any information would be greatly appreciated.