Port alerts indicate that you have a port open on your system that is also the default port used by the trojan whose name is mentioned in the alert. This is not a definitive indication that you have a trojan on your system.
If you are running TrojanHunter on Windows 2000, XP or 2003 TrojanHunter will show you the name and process identifier (PID) of the program that is using the port. You can use this to determine whether the alert is something that needs further investigation. (For example, if the port alert says "Port being used by process AIM.exe/PID 1024" you would know that this is your AOL Instant Messenger Client and could ignore the alert.)
If you are using TrojanHunter on Windows 95, 98 or Me TrojanHunter will not tell you what program is using the port. Use a utility like TCPView from SysInternals to find this information.