I'm sorry but, the only known causes for buildings that appears only when getting close, are those I've already suggested: compatibility first, or video settings or fsx.cfg settings, or transparency antialiasing.
The last suggestion is because some users reported success by repairing the FSX SP2 (or acceleration Pack) installation.
The only thing you can be sure of, it's not how the scenery is made and, if you have both the Addon Manager and the Couatl menus inside FSX, it means the software is running properly. If if wasn't, you wouldn't see buildings in any conditions, not just when you are at a distance.