So that shouldn't simply happen.
Try to enable Logging, Restart and Rebuild the cache, then exit and check the Couatl.LOG made immediately after the cache rebuilding session. It should tell you something about the visibility you set.
It is skipping over it totally maybe a problem with an airport code that has a number on it?
Here is my addons ini section
airport_visibility_zssy = 0
airport_visibility_zscb = 0
airport_visibility_ypd1 = 0
airport_visibility_yxdh = 0
and here is the log
Added Menu SubItem "Show GSX Menu by-passing YouControl Shift+F11" (parentId 82, id 94)
Airport visibility range for 'zssy' set to 0 miles
Airport visibility range for 'zscb' set to 0 miles
Airport visibility range for 'yxdh' set to 0 miles
User collision geometries reloaded