The problem is caused because if the scenery buildings have crashboxes, the ground level is on their roof so, when GSX creates an objects in the default position, and if the default position (which is completely unaware of the 3d buildings) is inside the building crashbox, the vehicle will be placed on the roof, because the ground level is there.
That's why it's possible to customize the default starting position for all vehicles at all gates, which is done through an airport profile so, if you don't what to do that, you might search if somebody has made a custom GSX profile for that airport, which should hopefully fix that.
