When you see misplaced gates positions, the cause is never GSX, and it's always the AFCAD from another scenery in conflict.
The most common source of conflicting AFCAD are files supplied with AI Traffic products, like MyTraffic or Traffic X, which are supposed to be used only as an enhancement of default airports, but must be removed if you have an addon airport.
Check the GSX parking customization page: it will tell you the full path name of the AFCAD used by GSX, which will help you understanding a possible conflict.