Then I just copied both directories Zurich and Zurich_terrain to the Windows 7 64-bit Computer and activated it again - result: No CTD's anymore! Not elegant at all but effective...
If this worked for you, then it's ok, but I can only repeat and confirm the crashes cannot be caused by the installer.
With regard to the scenery folders, the ones you manually copied, the installer does exactly the same thing. It copies them and activates the in the Scenery Library. The files are exactly the same and, if you don't believe it, you can easily verify this, by making a file comparison of the scenery folders as copied by the installer vs manually copied, you'll see they are exactly the same so, obviously, there can't be any difference here.
The installer has self-integrity checks so, if your download was corrupted in some way, the installer would abort. And, of course, if the installer was corrupted, it would be under XP and Windows 7 so, fact you were able to install under XP, clearly means the installer you downloaded was fine.
The only thing that might happen in the installer and could be different between the two OS, is the automatic addition to the Scenery Library, since XP puts this file in a different folder than Windows 7. However, if this was the case, and the installer under Windows 7 was unable to automatically add the scenery to the Library, you would noticed that, because you wouldn't see Zurich being added.
Since the installers are fully compatible with 64 bit OS, and nobody ever reported this problem, the only possible explanation is that something on your FS9 under Windows 7 is not the same as in XP, maybe the scenery.cfg has a syntax error (because of have hand-edited it or other addons having corrupted it), but this usually results in no scenery added automatically to the Scenery Library, but you haven't said anything about it.