Altitude problems like that are always caused by 3rd party Mesh sceneries. Opposite to any other kind of scenery, a Mesh scenery DOES NOT respect the layering of the Scenery Library. Instead, the Mesh with the highest nominal resolution will always "win", no matter the priority.
In any case, looking at your scenery.cfg, it shows you have all the OrbX areas on an higher priority than the airports, and this is surely wrong. Airports should always be on top of everything else, which is where our installers puts them by default.
However, for the reasons explained above, it's not sure this will fix the problem (although you should do it anyway), because if a Mesh has an altitude problem, and it has an higher resolution than default, it will affect an airport regardless how low its priority.
