I'm getting a similar issue. only difference is half the gate is showing
You either have an AFCAD in conflict, or an old .INI you made which must be removed.
This new GSX is causing nothing but problems.
None of these are GSX problems. GSX cannot automatically fix or look for conflicting sceneries, there are other utilities that can help you doing that. And, it would be WRONG if GSX automatically removed any customization .INI file you might have made in the past. We don't remove any of your files, it must be your choice.
Then when we try to go back to GSX level 1 its the same ol song and dance.
You "trying to go back to GSX Level 1" is another possible reason of this problem. The latest version of JFK which you'll get automatically with a Live Update REQUIRES GSX Level 2 to work, and its AFCAD and its .INI file are made assuming you have GSX Level 2 installed. Going back to GSX Level 1 is the wrong solution, caused by the wrong assumption Level 2 has "problems", but they are something else entirely.
There is no other conflicting scenery or afcad.
If you are sure of this, then the problem is caused either by an old .INI file you made for KFJK that you haven't removed, or by you trying to "go back" to GSX Level 1, with JFK now requiring Level 2.