What exactly were you trying to run? X-Term as above? If you are doing "interface=com.nokia.xterm method=run_command" and as the argument an application that will open a new window,you will get X-Term and then the whatever new window as requested.

However, if you have a command line app like "sh" as the argument of X-Term, or use com.nokia.HildonDesktop.AppMgr->LaunchApplication to run commands, there should be only one window.