You are probably experiencing an inactivity timeout that is built into Windows 2000, and 2003.
Microsoft has a Knowledgebase article referring to this problem. Go here http://support.microsoft.com/kb/297684
Be advised, you will be making registry changes by hand. Working in the registry can be very detrimental to your server if done improperly.
With that said, I would advise using the registry editing method and not the Command Line method. I have tried both in my time and have much better success and speed with the Registry editing method.
Hope this helps,