I think you might be misunderstanding the "Save Default Skin" function on the clipboard menu.
This function creates a subfolder for the aircraft under the "Skins" folder in the AHIII installation folder. The folder contains all the skin files for the aircraft's default skin; these are used by the skinner as a starting point when creating a new custom skin.
What it does not do is make a particular custom skin you like to fly with the new "default" skin choice for that aircraft - if that's what you're thinking it does...