TWR CTLR CLRED C421 OFF RWY 13R AT JFK; THEN 2 MINS LATER CLRED A BA31 OFF THE SAME RWY ON THE SAME SID. INITIAL SEPARATION BTWN THE ACFT ON HDOF TO DEP CTL WAS 3 NM WHICH IS ALL THAT IS REQUIRED. DEP CTLR TURNED THE C421 TO AN EASTERLY HDG AND WAS OVERTAKEN BY THE BA31 CAUSING A SYS ERROR.

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I CLRED THE C421 FOR TKOF ON RWY 13R; THE ACFT DEPARTED ON AN ASSIGNED HDG OF 140 DEGS; CLBING TO 5000 FT. APPROX 2 MINS LATER; I CLRED THE BA31 FOR TKOF ON RWY 13R; THIS ACFT ALSO DEPARTED ON AN ASSIGNED HDG OF 140 DEGS; CLBING TO 5000 FT. BOTH ACFT WERE SWITCHED TO DEP CTL WHEN AT THE DEP END OF THE RWY. WHEN I OBSERVED BOTH ACFT ON RADAR; EACH WAS INDICATING A GND SPD OF APPROX 140 KTS; SEPARATED BY 3 MI INTRAIL; BOTH APPEARED TO FLYING A HDG OF 140 DEGS AND 3 MI WAS BEING MAINTAINED. SUBSEQUENTLY I OBSERVED THE C421 TURNING TOWARD THE ENE. THE BA31 CONTINUED ON WHAT APPEARED TO BE THE 140 DEG HDG AND OVERTOOK THE C421 AS IT TURNED. BOTH ACFT WERE AT APPROX 4000 FT WITH WHAT APPEARED TO BE LESS THAN 3 MI LATERAL SEPARATION. I FEEL I GAVE ADEQUATE SEPARATION FOR THE DEP CTLR. WITH STRONG WINDS OUT OF THE SSW; I BELIEVE THE C421 WAS VIRTUALLY 'BLOWN BACK' INTO THE FACE OF THE BA31. UNDER THE CONDITIONS; A MORE EASTERLY HDG TO THE C421; PROVIDED BY DEP; WOULD HAVE BEEN MORE PRUDENT; BUT BOTH ACFT WERE NOT UNDER MY CTL. OTHER DUTIES PREVENTED MY NOTICING THE IMPENDING LOSS OF SEPARATION ON THE PART OF DEP CTL AND PASSING ALONG AN ADVISORY TO THE DEP CTLR.