What do you mean by the same area of JFK?
In the same geographical area.
I used to have Simflyers' JFK installed, but I removed it, along with the scenery.cfg entries for it
Some sceneries don't simply put files in their own folder, but they also put things in the general FS scenery folders. I don't know if this is the case for Simflyers JFK, but even if it's not, you still might have some files, usually leftovers from other installations (freeware sceneries often have manual install instructions an no installer/uninstaller) that still reside in the FS general folder, and might affect another scenery, even if their own scenery area has been removed. The very presence of a BGL in one of the main scenery folders might still affecting other sceneries.
I do recall also that Simflyers used flatten commands in the scenery.cfg, which is something that is not needed anymore in FS9 (it's an FS2002 technique). Check these as well.
Nothing else here that would seem to impact JFK, other than Imaginesim's LGA and EWR, but surely you don't expect me to uninstall those?
Assuming these don't put anything outside their own scenery folders, you might at least *try* to disable them in the scenery library. At least we KNOWN it's them. LGA is so close, that a conflict might be very possible.