Yes, I was just replying to you:
- the difference in FSX was because you had JFK V1, not V2
- the problem in Prepar3D is caused by ANOTHER scenery in conflict.
As explained many times on the forum, whenever you see "double something" with default buildings mixed in, it's never a problem of the scenery itself, and it's always caused by another AFCAD from another scenery (those buildings comes from there). The most common causes are AFCAD supplied with AI traffic packs such as My Traffic or Traffic X.
Use the free FSX Airport Scanner to search for AFCAD duplicates and remove them.