What makes you think you are supposed to have a .PYE file for EACH of your installed addons ?
Those are JUST some customization files that WE made for some airports, the list is the same on everybody's installation, and doesn't have any relationship to what you have installed, but only indicates which 3rd party airports have a customization file made by us, to fix obvious errors like altitude problems, fake jetways, etc. They are loaded only if you go to that airport, assuming you installed it.
As discussed in other threads about the missing parking spots message, the first thing to check is what AFCAD GSX is using for an airport, and if it's not the correct one, there might be a reason why the correct one hasn't been selected, for example if there are several additional fictionary ICAO codes used together with the main airport, to represent smaller bases, seaplane bases, etc.