Saving prefs on dedicated server

Greetings all.

I'm feeling really stupid at the moment because I cand seem to crack this, but here goes...

On a stock 1.4 implementation I am trying to get a server running properly. I have 2 directories.. both identical, one called Torque server and one called Torque. (was trying to immitate a server on one machine and a client on another).

If I go into server and start a dedicated server, then go into torque and start a client, I can see the game on the Lan and the master server and connect to it and play fine, but when I close the server no prefs get saved in the server.

I have the dos window and the only way to seem to close it is to close the window, so it never gets to go through exit to save the pref files.

This means that any new server prefs I set up during game play or change never get saved on the dedicated server as closing the window just ends the process it doesn't "close" the server properly.

Is there a way I should be closing the dedicated server from the dos window without just closing the window, or am I missing something fundamental?

Regards

Graham Evans