This issue manifests only when JavaScript is used to close the control (i.e., oWnd.close()) and the [x] button in the titlebar works as expected. Clicking the handles makes the popup element visible, but it is not responsive (i.e., buttons in its titlebar cannot be clicked, it cannot be dragged, etd.).
A workaround is to add the following OnClientClose handler:
function OnClientClose(oWnd, args) {
	//hide remaining resizing handles in Lightweight render mode
	if (oWnd.view && oWnd.view.resizable && oWnd.view.resizable.repaint)
		oWnd.view.resizable.repaint();
	//other logic
}

A fix will be available in the Q1 2014 release.