Like the others said, when you call net stop, it will invoke the OnStop in the Windows Service. If the OnStop does not kill all the threads in the app, or doesn't shut everything down properly, your service might not stop. (I've seen this happen in one of our WCF services: we didn't close the ServiceHost in OnStop, and therefore, the app would not stop at our command - we'd have to kill the process by hand.)
One common pattern I've seen is to try calling stop on the service, and if it doesn't die within a timeout (10 seconds), kill the process by force. As an alternative to batch files, PowerShell has some pretty good support for dealing with services.