You cannot be sure of using the latest GSX version, just because you downloaded its installer. It depends when you downloaded it, and when installed it, since lots of stuff is updated on the fly.
In order to have the version of the program that automatically skips auxiliary airport with no parkings, you must have installed it after June 6th, as explained here:
http://www.fsdreamteam.com/forum/index.php/topic,13662.msg101840.html#msg101840If you are sure of this, then you should check the AFCAD used by GSX in the parking customization dialog, to see which is the file that gets in the way of the main airport which, perhaps, has at least one parking, so it won't be automatically discarded by GSX, but must be manually disabled, as explained in the previously linked post.