When you open an instance of the application, make sure you are not opening a reference to LabVIEW, but to your stand alone application. In order to do this, you need to make sure your application is registered with the windows system. You can do this by either running the installer for it, or by running the executable with /register after it in the command line. In your code, you should create an instance of the application, then an instance of a VI pointer and use the GetVIReference method to assign a VI object reference to the pointer.