Thanks Handy,

Just incase someone else has the same problem I had to do this in the Application_Startup:

  private void Application_Startup(object sender, StartupEventArgs e)

  {

            this.RootVisual = new MainPage();

            UXShell.Current.IsInitializing = true;

            //  create a new ApplicationPackage that represents App1

            ApplicationPackage app3 = new ApplicationPackage()

            {

                ID = "SimpleExternalApp",

                Name = "SimpleExternalApp",

                Source = new Uri("SimpleExternalApp.xap", UriKind.RelativeOrAbsolute),

                  EnableMetadataDiscovery = true,

                MainType = "SimpleExternalApp.MainPage",

                VirtualPathIdentity = "/SimpleExternalApp",

                Size = -1 // auto detect the file size at runtime

            };

            UXShell.Current.Applications.Add(app3);           

            UXShell.Current.IsInitializing = false;

        }

Thanks again.

Ajay