I will have to try and replicate the conditions and post a screen shot.
No need for it, your explanation now is clear enough. You don't have any lights so, no need for a screenshot, I believe you don't have any lights on your system, but this is not how the scenery is made.
Total black with 22L being fully lit.
Then in this case the problem doesn't have anything to do with the scenery, but it has been caused by another scenery in conflict.
JFK uses standard FSX lights in the AFCAD, nothing fancy like custom lights and similar, which might not working for a number of reasons. Since they are made with standard FSX commands in the AFCAD, it means the most likely cause of the problem is a conflict caused by the AFCAD of another scenery, or another product that comes with AFCADs, like Traffic packages, etc.