Actually the "windowed mode" seems not to work in FSX under win7 64. FSX always is "Full Screen".
That's odd: I've just tested Win 7 64 (on a Mac notebook with an nVidia 9600), and Windowed mode works just fine, just as in Vista or XP. Not only that: our registration window doesn't have the slightest issue and is perfectly visible, both in Windowed mode and in Full Screen mode.
So yes, it looks like a video drivers issue.
However, you did it correctly: the registration window doesn't do anything strange, except than simply inserting your Serial number in the registry for you so, it's doesn't make any difference, if you put it yourself with regedit.