This is normal and it's by design. GSX never supported loading data from multiple .BGLs at once, it only uses one file, which must be self-contained, with all elements required by GSX (parking spots, taxiways, runways, etc ) all in the same file.
Some developers (mostly freeware), might not release a complete airport but, instead, only enhancements and additions to the default, for example adding objects or buildings. These files might not contain any elements used by GSX, so in this case GSX should ignore the file.
When a .BGL is designed to be an add-on for the default, it doesn't use the various "DeleteAirport" instructions in the .BGL, because it was designed to work together with the underlying default. Instead, a scenery that includes everything, *should* use these DeleteAirport commands, to be sure there wouldn't be any conflicts with the default airport. Almost all add-on airports are usually made this way, but some aren't and, since the absence of a DeleteAirport command is the clue GSX use to detect an airport that is supposed to work together with the default, it skips the file and revert to the default in these cases.
This is another issue that should change in the future, when the new API from SU10 will be out of Beta, assuming it will be also updated to add some things we are sill missing and we obviously asked to Asobo to be added ( data about Jetways, Jetway links and Runways Starts are missing in the current Beta ), we might possibly get away with the airport cache altogether, solving lots of issues and being able to read encrypted airports as well.
