That's not a bug but, instead, it's a new feature, which is explained at Page 70 of the GSX Manual but briefly, it's done for TWO reasons:
1) Since P3D V5 doesn't support custom textures, if you download a GSX profile made for P3D V4 that uses custom textures and load it in P3D V5, instead of giving you an error (the first release with the new multi-livery support did that ), it will scan the file, and remove all references to custom textures, reverting to default operators at those gates. And, as soon as you EDIT the file, it will save it to a new file, but flagged as being for P3D V5 only. This way, it won't touch your original profile, in case you also use P3D V4, which will load its version instead.
2) Since the default database has changed quite a bit from P3D V4 to V5, in order to prevent malfunctioning profiles due to different gate assignments, if the name of the .BGL starts with APX* ( all default airports have such names ), GSX assumes it's a default airport so, it also set itself in a way that, as soon as you try to edit it, it will save it back as being V5 only, so P3D V4 won't load it, something that in previous versions would have ( the name of the .BGL is the same ), causing problems because of the changing gate assignements.