Try with different Mesh density settings. We usually found 10 meters resolution and 100% complexity is ok for most uses.
And, of course, try with the Megascenery turned off. That scenery has just been released, while JFK is out since 2008, I guess if there compatibility problems, it would be their duty and their best interest too (considering that *everybody* has JFK...) be sure that scenery is compatible with our own.