I still have exactly the same problems with ILS RWY 4L - from the first Version of FSDT KJFK on up to the newest Version 2.1
As I've said, The ILS works correctly, as the previous screenshot confirms.
Your problem is surely caused by another scenery in conflict and of course, since it was caused by another scenery, it's still there regardless if you install JFK V1 or V2.
The most common source of AFCAD conflicts are AFCAD coming from AI Traffic packages, use the free FSX Airport Scanner program to find AFCAD duplicates at KJFK but note that, if that program doesn't report anything, it doesn't mean you don't have a scenery conflict, because a misplaced ILS can also be caused by a non-AFCAD scenery, and these must be searched for manually.