OK look... I disabled EVERY piece of scenery, mesh I have, and with KJFK only, I still have raised water and the fence problem at that place. Looks simply odd.
Then I did a 2nd test, KJFK OFF, default scenery only - no raised water and no fence in the air.
3rd test, UTX USA on, no FSGlobal... still no raised water nor fence in the air.
4th test, add FSGlobal... still no raised water nor fence in the air.
Even tested with full mesh quality, and had no problems really.
And finally... KJFK on... raised water, fence in the air.
IMO the flatten is not correctly positioned, and it reaches too far out, into the water, and doesn't reach around the fence, or the fence is positioned wrongly. Whatever... I ain't the scenery developer.
Can't this be solved differently? The default KJFK scenery doesn't have harsh walls around the airport, even at the highest mesh, and this being one of the arrivals I actually use quite often, I hate seeing the "water-wall" just before touchdown!