This is usually caused by GSX not reading the correct AFCAD for that scenery, usually because there's another one in conflict. The most common cause of conflicting AFCADs are those that comes with AI Traffic package.
The GSX parking customization page will tell you which AFCAD is used by GSX.
If the AFCAD used belongs to the scenery, it might stil not the correct one, for example in case of additional helicopter bases, seaplane docks, etc.
The GSX manual explains, at page 24, the airport_visibility command, which is required to deal with scenery developers that add auxiliary airports with fake ICAO codes, usually helicopter bases, seaplane bases, etc.
