If you don't want to get the Controller status window displayed, please set the Notes.ini parameter: "ShowControllerStatusWindow=0".
By default, the window will be displayed.
NServer.exe is using the Notes.ini parameter ShowControllerStatusWindow=0 before the controller is started, but the NService.exe is not. Specifically, the Notes.ini parameter ShowControllerStatusWindow=0 works only with the NServer.exe and not with NService.exe.