When you see a difference in gate positions, it's usually because GSX is not using the AFCAD that comes with the scenery. The most likely cause, it's another AFCAD in conflict, but it's also possible the AFCAD that comes with the scenery might have been discarded because of some problems with it.
So, the first thing to check, is which AFCAD GSX is currently using, which can be done by opening the scenery customization page.
