GSX obviously use the gate numbers as they come from the scenery itself, since it reads its AFCAD file.
This might match the charts or not, depending which charts you use and if the scenery was made using the same charts. This won't be any different regardless if you used or not GSX. If the scenery doesn't match your charts, not even the default ATC controller would assign you to gate matching them.
So, normally, GSX will match the SCENERY exactly as it is so, you are supposed to see the same gates as you would if you used the standard "World->Go To Airport" menu.
If they don't match, then you have another problem, which is GSX using a different AFCAD than the one that comes with the scenery, which is not normal, but might happen if you have conflicting AFCADs, which is something you should try to prevent.
You can check which is the name of the AFCAD used by GSX, and be sure it's the one that comes with the scenery you are using.