I am referring at opening the FSX, when you install a new scenery usually create and update the scenery database
Ok, sorry, I tought in fact you were referring to the final load step.
Alright, this is an entirely different problem, and I'm quite sure it doens't have anything to do with our sceneries, it probably something else that caused a problem that needed a new scenery to be installed to be triggered.
You might first try to do the following:
Browse your FSX folder, than go to any scenery folder (which one doesn't matter), and delete the included SCENERY.DAT file. This will trigger another refresh of the scenery database on the next start and perhaps just fix the problem.
Another possible fix might be to check your scenery.cfg file, located at:
%ALLUSERSPROFILE\Microsoft\FSX
and go to the JFK area, then change Active=TRUE to Active=FALSE. This will disable JFK, and will trigger another Scenery Database update. If FSX would still crash, at least you know is certainly not JFK that caused the problem. If FSX would run instead, do not automatically assume it was JFK, but re-enable it instead! It might be that, a further rebuild of the Database might finally fix the problem.