Is this computer always logged on? or at least 99% of the time?
If so, just make a shortcut, drop it in the autostart folder, and add -nogui to the end. It is invisible like a service, but it starts up every time for sure.
Also..
In Windows/NT 4.0 go to the Control Panel->Services function. In Windows 2000 go to the Control Panel->Admintrative Tools->Services function. Edit the start properties of the setiqueue service to be what you want, and start the setiqueue service.
Do not set the service to interact with the desktop. When SetiQueue is used as a service it expects to run in the background and does not enable any of its user interface functions.
Just make sure it is set to startup automatically, etc