Whenever you have a difference between the scenery and GSX, you should first check if the AFCAD read by GSX is the one which is supposed to be the correct one for the scenery. You can do that by looking at the parking customization page in GSX, which lists the name of the AFCAD used by GSX.
Note that, if you have "partial" AFCAD files, meaning a file that only enhances the default one (several freeware sceneries are made like that), GSX won't use it. In order to have GSX use an AFCAD, the file must be self-contained, which means it must contain at least the taxiways and all the parkings.
