joelflorendo,
In a word, No, your not missing anything.
The modal IE window does not register as it's own application so the code in the FAQ ([tt]GetIEApp[/tt]) doesn't see it.
I spent about 30 minutes digging around MSDN and I can't figure out where the modal window is registered, so I have no idea how to get to it from the window it was spawned from.
I got the impression from the literature that you can reference the objects on the modal window as if they exist on the source window (IE Application) but that just doesn't sound right to me and I don't have time right now to build some dummy pages to test it.
Sorry I don't have more information for you...
CMP