Solved! Go to Solution.
<info>widgets/InfoTemplates/InfoPopupWidget.swf</info>
<info>widgets/InfoTemplates/InfoPopupWidget.swf</info>
Thanks for pointing me in the right direction. Now my popups look much cleaner. Anyone else that runs into this problem will want to look in QueryWidget.mxml and follow infoTemplate:IInfoWindowTemplate and look at the override public function showInfoWindow() and infoReady function. This should help you fill in the gaps a little.
Thanks,
Tyler Waring