<?xml version="1.0" encoding="utf-8"?>
<mx:WindowedApplication xmlns:mx="http://www.adobe.com/2006/mxml" layout="absolute"> 

    <mx:Script>
        <![CDATA[
            import mx.core.Application;
            import mx.core.Window;

            private function openPopupWindow():void
            {
                var alertWindow:Window = new Window();
                alertWindow.title = 'Alert Window';
                alertWindow.width = 400;
                alertWindow.height = 200;
                alertWindow.open();

                centerWindow(alertWindow);
            } 

            private function centerWindow(window:Window):void
            {
                var screenBounds:Rectangle = Screen.mainScreen.bounds;
                var nativeWindow:NativeWindow = window.nativeWindow;

                var mainNativeWindow:NativeWindow = Application.application.nativeWindow;
                for each(var screen:Screen in Screen.screens.reverse())
                {
                    if(mainNativeWindow.x > screen.bounds.x)
                    {
                        nativeWindow.x = mainNativeWindow.x +
                                             (mainNativeWindow.width - nativeWindow.width)/2;
                        nativeWindow.y = mainNativeWindow.y +
                                             (mainNativeWindow.height - nativeWindow.height)/2;
                    }
                    else
                    {
                        nativeWindow.x = (mainNativeWindow.width - nativeWindow.width)/2;
                        nativeWindow.y = (mainNativeWindow.height - nativeWindow.height)/2;
                    }
                } 

                nativeWindow.x = (screenBounds.width - nativeWindow.width)/2;
                nativeWindow.y = (screenBounds.height - nativeWindow.height)/2;
            }
        ]]>
    </mx:Script>
    <mx:Button x="10" y="10" label="Open popup window"
        click="openPopupWindow()"/> 

</mx:WindowedApplication>