Hi,

I stumbled onto the answer.

It has to do with the scaleMode.  In the following code example if, noScale is commented out the jpg doesn't appear to be added.  When I altered the test to add a SWF, I saw the oversized SWF which led me to test the scaleMode. 

import flash.events.MouseEvent;
import flash.display.Loader;
import flash.net.URLRequest;
import flash.net.URLLoader;
import flash.events.Event;
import flash.display.MovieClip;
import flash.display.Sprite;

var screenBounds:Rectangle = Screen.mainScreen.bounds;
var screenWidth:Number = screenBounds.width
var screenHeight:Number = screenBounds.height

stage.nativeWindow.x = Math.floor((screenBounds.width - stage.nativeWindow.width)/2);
stage.nativeWindow.y = Math.floor((screenBounds.height - stage.nativeWindow.height)/2);

var AppLoader:Loader = new Loader();
AppLoader.load(new URLRequest("test.jpg"));
AppLoader.contentLoaderInfo.addEventListener(Event.COMPLETE, reportComplete);

var holderMC:MovieClip;

function reportComplete(event:Event) {
trace("COMPLETE")
holderMC = new MovieClip;
//holderMC.addChild(AppLoader.content)
//addChild(holderMC) // works as does addChild(AppLoader) or addChild(AppLoader.content)
openWindow()
}

function openWindow():void {
var initOptions:NativeWindowInitOptions = new NativeWindowInitOptions();
initOptions.systemChrome = NativeWindowSystemChrome.NONE;
var newWindow:NativeWindow = new NativeWindow( initOptions ); 
           
newWindow.width = screenWidth-100;
newWindow.height = screenHeight-100;
newWindow.x = 50
newWindow.y = 50

newWindow.stage.align = "TL";

newWindow.stage.scaleMode = "noScale"; //If commented out the jpg disappears

newWindow.stage.addChild(AppLoader.content);

newWindow.activate();
}