[etc]

Удалять попап надо. Кстати, описанной ошибки я получить не смог.

<?xml version="1.0" encoding="utf-8"?>
<mx:Application xmlns:mx="http://www.adobe.com/2006/mxml" layout="absolute">
 <mx:Script>
  <![CDATA[
   import mx.controls.Button;
   import mx.effects.effectClasses.ZoomInstance;
   import mx.effects.Effect;
   import mx.containers.Panel;
   import mx.managers.PopUpManager;
   import mx.core.IFlexDisplayObject;
   public var i:int=0;

   
   public function cr():void{
    var p:Panel=new Panel();
    i++;
    p.name='window_'+i;
    p.title='Lex_'+i;
    p.width=150;
    p.height=100;
    p.x=int(Math.random()*(screen.width-p.width));
    p.y=int(Math.random()*(screen.height-p.height));
    var b:Button=new Button();
    b.label='min';
    b.name=p.name;
    b.addEventListener(MouseEvent.CLICK,min);
    p.addChild(b);
    PopUpManager.addPopUp(p,this);
    //this.addChild(p);
   }
      
   public function min(e:Event):void{ 
	var win:Panel = (e.target as Button).parent as Panel; // :-)
	PopUpManager.removePopUp(win);
	WinBar.addChild(win);
   }
   
  ]]>
 </mx:Script>
 <mx:Button x="25" y="22" label="Создать окно" click="cr()"/>
 
 <mx:ApplicationControlBar height="75" id="WinBar" width="80%" horizontalCenter="0" bottom="10">
 </mx:ApplicationControlBar>
</mx:Application>