Date: 201509
Local time of day: 1801-2400
Location: JFK.Tower, NY
Light: Dusk
Aircraft: Widebody; Low Wing; 2 Turbojet Eng
Operator: Air Carrier
Operating under: Part 121
Flight plan: IFR
Mission: Passenger
Flight phase: Final Approach
Airspace: Class B JFK
ATC / advisory: Tower JFK
Second aircraft: Large Transport
Reporter organization: Government
Reporter function: Local
Reporter qualification: Air Traffic Control Fully Certified
Human factors: Communication Breakdown; Distraction; Confusion
Anomaly: ATC Issue All Types; Conflict Airborne Conflict; Deviation - Speed All Types; Deviation - Track / Heading All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Deviation / Discrepancy - Procedural Clearance
Detector: Person Flight Crew
When detected: In-flight
Result: Air Traffic Control Provided Assistance; Flight Crew Executed Go Around / Missed Approach
Contributing factors: Procedure; Airport
Primary problem: Procedure

Narrative: Runway 4L/22R has been closed at JFK do to a major reconstruction project. The return of the runway has been delayed. In the fall; the wind has a greater tendency to come from the NE; which prevents us from using our standard VOR 13L departure 13R overflow VOR/DME 22L. Usually we would use 4L and 4R but again; 4L is still closed. So instead we use VOR 13R depart 13L overflow ILS 4R. This creates an extremely difficult operation which I have seen 3 times in my career; twice in the past week including today. The complexity is due to airspace design and airport design. This complex configuration is what we were doing.I was working LC2; which at the time was handling Runway 13R and Class B Airspace traffic; all which must be handed off do to the UN delegation taking place in NYC. My VFR traffic at the time was taking a very unusual route to get around the Class B airspace and to avoid the UN TFR'S. This was unusual traffic who was passing underneath our approach and departure corridor; and did require a lot of my attention. Aircraft Y was #1 and cleared to land 13R. Aircraft X had an 80 knot overtake and was not calling the tower. Aircraft X was operating on an 'S' tag; an approach scope I have no way of contacting with my ETVS (Enhanced Terminal Voice Switch). I began to get the coordinators attention when Aircraft X checked in on the wrong tower frequency. This is a common mistake because N90 has a difficult time having the arrivals contact 123.9; since they so often call 119.1 on the reciprocal runway configuration. The controller on LC1 119.1 instructed Aircraft X to begin reducing airspeed and call my frequency. At this time I lost radar separation and instead relied on visual; I had both Aircraft Y and Aircraft X in sight on approach. During the time Aircraft X was changing frequencies; I instructed Aircraft Y to exit the runway as quickly as possible for traffic in trail. When Aircraft X checked in on my frequency; they had not begun to reduce airspeed. I instructed Aircraft X he was #2 and cleared to land RY 13R and to reduce to final approach speed. My plan was to wait to see how Aircraft Y rolled out; and if they didn't exit promptly; to send Aircraft X around and fly heading 130 and pass well over the threshold of runway 4R.Aircraft X responded but I could not understand what he said. So I repeated the clearance to land and mid transmission; I realized Aircraft X was in a hard right turn taking themselves off the approach; and converging towards the approach to runway 4R. Traffic on approach to 4R was level at 1;500. I instructed Aircraft X to fly heading 150 (which is about what they turned to themselves) and to climb to 3;000. I then pointed out traffic to Aircraft X; a Boeing 757 on approach to runway 4R. Aircraft X had them in sight; but Aircraft X was not climbing. I was reluctant to turn Aircraft X more then they had turned themselves as I was not very confident that an aircraft of that magnitude could turn as tight as I needed in such a small space and short amount of time. I then instructed Aircraft X to 'begin to climb; now.' After hearing this; Aircraft X climbed very well; and was at 2;800 when he passed over the B757 at 1;500. Aircraft X asked to continue their climb to 4;000; and I approved that. After this; I asked to be relieved from position.I can't really comment on the runway reconstruction project and progress; so I won't.We should not be on this runway setup. Not only is it complicated; but we use it so infrequently that everyone involved is not very good at it. This is evident from my report alone; the wrong frequency issued by N90; Aircraft X's failure to reduce airspeed adequately and their extreme turn off final; and my own failure to provide better control instructions away from the 4R final in an unusual situation.Traffic to JFK should be delayed when winds are forecasted to be like they are today; so that one runway can accommodate the arrival demand.




Synopsis: JFK Tower Controller reported a loss of separation that he attributed to the runway configuration the airport was on. Controller had a loss of separation due to speed of second aircraft being 80 knots faster than the preceding traffic. Controller did not send aircraft around but tried to get visual separation. Aircraft went around on its own and turned into parallel traffic which Controller had to separate it from.