I do see both the Couatl and Addon Manager menus in the simulator, and to my understanding that means everything is running correctly, however, buildings at JFK still do not appear.
Yes, if you see both menus, it means all the software is running correctly. Nothing related to the program running, antivirus, etc.
Has the scenery being added to the Scenery Library ? Have you seen installation errors about any problem with your scenery.cfg ? If your scenery.cfg already had an error before installing our product, the installer will warn about this and since it can't modify a corrupted file, it will abort, so no scenery will be installed.
Are you running Vista or Windows 7 and using FSX into any of the "Compatibility" modes ? If yes, turn them off, because this won't work.
Also, check if you have the following file:
%APPDATA%\Virtuali\Couatl.err
If you have it, post its contents here