As I suspected, your FSX.CFG had an error, a "hole" in the Simobject numbering, so our installer won't touch it.
See this section:
SimObjectPaths.0=SimObjects\Airplanes
SimObjectPaths.1=SimObjects\Rotorcraft
SimObjectPaths.2=SimObjects\GroundVehicles
SimObjectPaths.3=SimObjects\Boats
SimObjectPaths.4=SimObjects\Animals
SimObjectPaths.5=SimObjects\Misc
SimObjectPaths.8=C:\ProgramData\12bPilot\SODE\SimObjects
SimObjectPaths.6=C:\Program Files (x86)\12bPilot\SODE\data\SimObjects
The number 7 section is missing, which is a mistake. It should be like this:
SimObjectPaths.0=SimObjects\Airplanes
SimObjectPaths.1=SimObjects\Rotorcraft
SimObjectPaths.2=SimObjects\GroundVehicles
SimObjectPaths.3=SimObjects\Boats
SimObjectPaths.4=SimObjects\Animals
SimObjectPaths.5=SimObjects\Misc
SimObjectPaths.6=C:\ProgramData\12bPilot\SODE\SimObjects
SimObjectPaths.7=C:\Program Files (x86)\12bPilot\SODE\data\SimObjects
I'm sure that, if you fix it and reinstall GSX, the installer will now add the proper line to it.