but when i try to start a bf2 server, nothing runs.
unless i start the bf2 server launcher manually, then we can connect to the server but cannot see it in gametracker or when we try to add it to favorites.
These sound like separate problems.
On the first issue, I haven't tried running BF2 on Windows 2008, so this is a tough question for me. But, have you tried running it as "administrator" instead of as the default service user? I know that this helped sometimes with Win2k3. Also, are you seeing any notices pop up from Windows about viewing the console?
When you say it's not running, is it that Windows is starting and immediately stopping the service? Is there anything showing in your Windows event log?
On the second problem, I suspect that you may need to specify the IP in your BF2 configuration. Windows 2008 has recently had problems with other servers when the IP isn't manually specified like this.