Why do you need to wait? How are you opening a popup before it's close anyway? The popup will be on top so if you click/tap anywhere besides the popup it will close so you shouldn't have to worry about it.
base on what i'm seeing here http://jquerymobile.com/demos/1.2.0-alpha.1/docs/pages/popup/ it looks like they don't go to display: none; Rather they are positioned VERY far off the page... like top: -99999px and left: -999999px... maybe you can check to see if its within the view port of the window and not some extreme negative value?
I'm telling you, it's asynchronous because if i put an alert after the popup('close') the alert is opened when the popup is still opened. The event does not help me either because i can't use it when i call 'close' specifically... it's a global event and that doesn't help me.