so you were running an in game dedicated server. With the batch files, it should speed up the server, as you don't have to load the GUI :D
Glad to see you got it worked out. You know to edit your config files so that you can rename the server, get listed on Gamespy, allow or disallow voting, add or subtract new and old maps, change the health decrease rate, spawn times, etc..
Each batch file you create should have a corresponding config file. The config file is very powerful as it even allows you to change some of the physics of the game, like run speed, shooting speed, ammo.. I even heard it allows you to change the gravity of the game, so you can have a floating fight too :D
however, I don't know how to change the physics..