It seems that after installing FSDT sceneries the terrain.cfg is messed up.
None of our installers change anything in the terrain.cfg, they never did such invasive thing before, and they are surely not doing it now.
I believe it must be some kind of bug of the default landclass which is called by JFK in that area (the default Marshes/Wetland), which seem to happen in P3D V3 too, so it's interesting nobody noticed it before, maybe if you have a 3rd party product in V3 which is still not available in P3D V4, this might have fixed the problem but, in V4, you are back with the default, bugged landclass.
In any way, you can fix it by removing the LC_2817.BGL file from the JFK scenery folder. We'll test it a bit more and, if it's ok, we'll make it official, so the Live Updater will remove the file automatically on the following runs.