When the "service.bat stop" operation is called from a working directory that is not the ./bin directory of the jboss installation, the script makes the server shutdown. This is because the service.bat script calls the 'shutdown' command. When the script is called from within the jboss/bin directory, this resolves to the shutdown.bat script. However when called from outside of the jboss/bin directory (a different working directory), the windows command shutdown is called instead. This causes the server to do a clean shutdown. While this will obviously make JBoss shutdown too, it's probably not what the caller of service.bat wants to happen.