There's no difference whatsoever from a default airport or an FSDT airport, in relationship to your ability to customize it. You are supposed to see all your gates, and customize them, just like a default airport.
Nobody ever reported a problem like that, the only possible explanation is that the airport .ini file has gone corrupted for some reason. Try to remove any .INI file named KFJK*.INI in your %APPDATA%\Virtuali\GSX folder (when FSX is closed), and try again.