Surely it's not a problem of the scenery, otherwise someone else would have noticed it by now, considering JFK has been released in 2008, and this is the first report.
So, it's likely you must have some conflict with AFCADs coming from other products, like AI traffic packages. Use the free ScanAFD program to look for AFCAD duplicates at JFK, and remove all the extra, except the default from MS and the one that is in the fsdreamteam folder.
Note that, it's possible that the ScanAFD will say there are 2 AFCADs for JFK in the fsdreamteam\JFK folder. If it does, don't remove anything in the fsdreamteam folder, it's all right, there are supposed to be 2 AFCADs, because one contains only Approaches so, it's not really a duplicate, it was made to allow editing the main AFCAD without touching the procedures, since AFCAD editors that were available back then weren't able to handle Approaches.
So, you need to search for duplicates only outside the fsdreamteam\JFK folder.