Sorry you are not able to see the white patched on the runway. When I click on the photo I can actually see it not exactly sure why it's not quite visible.
I cannot see it in my sim!! I can clearly see it in YOUR screenshot, which is why I said you have some kind of conflict.
Where and what files exactly should I be looking for in terms of duplicates. I want to make sure I remove the correct conflicting file(s).
As I've said, should first try the free FSX Airport Scanner utility to look for AFCAD duplicates. However, this would only find for AFCAD duplicates ( BGL file with airport data inside ). If you have another kind of conflict, like a mesh scenery, that utility can't help you, and you must find the file manually.
Do you see some difference if you change the Mesh Complexity slider ? If yes, then you would know for sure the issue is caused by a mesh scenery, maybe a global product, like FS Global, etc. not necessarily something related to the NY area.