If the scenery on that particular location is solid, which might also include the crash box for the building, the ground altitude there is not really on ground, so the VGDS ( or any other object created by GSX ), will be placed higher, because we need to place objects above ground ( otherwise they won't work on a sloped airport ), but in that particular point, the ground might be higher, due to the building crash box, which might not even be very precise.
Try to see if it works better if you move it farther from the wall, be sure you set the height from ground again, and restart GSX after exiting the editor.