Is it possible the scenery comes with two airport files ? The "airport-remove" name sounds like something made to remove something else, so possibly the "real" airport data might be in another file. GSX would have an hard time deciding which one to pick in these case.
But assuming this is the case ( I'm only guessing ), you can probably fix this by making a copy of the other airport file ( assuming there is one ) in the GSX profiles folder in %APPDATA%\Virtuali\GSX, so it will be used by GSX only.