I think it depends on how you add the popup, check the documentation:
http://livedocs.adobe.com/flex/3/langref/mx/managers/PopUpManager.html
create or add popup takes four parameters, and the fourth parameter is a child list
childList: String (default = null) - A child list to which you can add to pop up. One of PopUpManagerChildList.APPLICATION, PopUpManagerChildList.POPUP, or PopUpManagerChildList.PARENT (Default).
So, try adding all the popups to a specific child list, and then play around with the size of the list.
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