Timmy,
If the SIT server is able to open port successfully, netstat -na will show a TCP port 6011 in Listening state. Failure to open the port should cause an error dialog and is most commonly caused by another application already using the port. More information is needed to diagnose the problem, but make sure that no windows security feature is interfering (ex. windows XP SP2 network security setting)
It is not possible to start multiple ports in one matlab process. You will need to start multiple matlab processes and start server by typing 'NiMatlabServer('start',6012)' for example.
-SumitG