I figured out the problem. Look at where GSX thinks the KPHL AFCAD is located.
That's not what's happening here, GSX reads the KPHL AFCAD path correctly, I've checked it both with the KPHL.INI in the scenery folder and with the KPHL.INI in the %APPDATA% folder.
Note that, if you move the KPHL.INI from the scenery folder to the %APPDATA% folder, and vice-versa, any change on the scenery folder will trigger a cache refresh and, it's best if you use the "Restart Couatl" option from the Couatl menu after the cache is remade.
So, I confirm it's as I've said before: it seems the code that reads the KPHL.INI from the scenery folders isn't working, but if you put the KPHL.INI into %APPDATA%\Virtuali\GSX, it WILL work.
We'll surely fix this, the reason for having two places where the scenery .INI file is read from, is that you can further customize a scenery that comes with an .INI file in the scenery folder (like this one) but, since your tweaks will be stored in a new .INI file in the %APPDATA% folder (GSX couldn't write into the scenery folder anyway if it's under FSX, due to the UAC), if you want to go back to the .INI supplied by the scenery developer, it will be enough to remove the .INI in the %APPDATA% folder, and the one in the scenery folder will be used.