I can reproduce this 100% of the time with different popups, removing all MXML content and even blanking the skin so all you see is the modal effect of a blurred window. As soon as something happens, such as an advancing progress bar, whatever, in the underlying window, the app is frozen. Flash Builder shows no errors, just that the app is terminated.
When I step through I end up in some core windows resize stuff before the app goes away. Something else I should try? Known bug? I searched and didn't find much about popups.
Flex 4.6, Windows 7 Ultimate 64, lots of memory and all that—get the same behavior on two different Win7 machines but not on two different MacOS boxes.