Are you using an mx:Application or s:Application?
If you're using s:Application, you should be using <s:controlBarContent>...</s:controlBarContent> instead of <mx:ApplicationControlBar dock="true">...</mx:ApplicationControlBar>
Thanks I switched it out but my popups still show in front of the controlBarContent
You sure it did this in Flex 3? I think they were always parented by App
and thus obscurable.
You can request your popups go in the app's child list.