Certain interface or pop-up windows are works in progress, so the sim uses pop-ups from microsoft windows in their place.
This was happening in multiplayer too a couple of patches ago, when selecting what you wanted to fly you'd get a windows pop-up with the available options, but they have changed it and it now works from inside the sim's interface.
It still happens with tracks though: a windows pop-up will appear asking you where to save your file.
If you have disabled the aero interface (in win7 and vista) the pop-up can't be displayed and you get a lock up. The temporary solution is to enable aero until they change it to use the in-game interface.
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