That doesn't have anything to do with the scenery.
The parking spots are in the correct real-world location, if FSX is confused about which airport is in use in its own menu, that's nothing related to the scenery. An AFCAD doesn't have something like an airport "range", that developers can specify in order to prevent FSX being confused by two very close airports.
Instead, you can do something to prevent *GSX* to be confused by two nearby airports (but of course, it won't change anything in the FSX "Go To Airport" menu), as discussed here:
http://www.fsdreamteam.com/forum/index.php/topic,12126.msg92297.html#msg92297Since you can use GSX itself to position the airplane (using the "Just Warp me there" option), once GSX is prevented to be confused by two very close airports using the aforementioned method, you can simply ignore if the FSX "Go To Menu" is showing the wrong airport.