GSX surely correctly localize sceneries and their parking spots, regardless if they are default, freeware or payware, provided it finds and uses the correct AFCAD. The reasons why the scenery AFCAD is not used might be different:
- The AFCAD has errors, so it has been rejected and another one is used in its place
OR
- There's another AFCAD in conflict, so that is used instead
It's possible to check which AFCAD is in use by GSX by opening the "customize airport positions" menu and looking at the name of the AFCAD used.
If the name is not the right one, it's possible check why, by enabling Logging in the "Troubleshooting" section of the GSX Settings menu, and looking at the Couatl.LOG file that will be created in the %APPDATA%\Virtuali folder on the next startup.