ACR Y CLB TO WRONG ALT OCCUPIED ALT HAD LTSS FROM WDB. SYS ERROR.

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I WAS WORKING LCL WHEN ACR X CHKED IN FOR VOR APCH TO RWY 13L AT JFK. ACR X WAS INSTRUCTED PREVIOUS ARR HAD EXECUTED A MISSED APCH AT DECISION HT. I NOTICED ACR X GND SPD DROP TO 130 KTS AND ASKED IF HE COULD INCREASE 20 KTS FOR TFC IN TRAIL. ACR X REPLIED NEGATIVE. I ASKED ACR X TO SAY AIRSPD. HE REPLIED 145 KTS. I THEN CALLED ACR Y. THE PLT RESPONDED (LATER INFO SHOWED APCH TOLD THE PLT TO CONTACT ME 4 MINS PRIOR). I ISSUED ACR X 2 O'CLOCK 2 MI. ACR X CALLS HE IS ON A GAR. I INSTRUCT ACR X HDG 090 MAINTAIN 2000. I INFORM ACR Y OF ACR X TFC IS ON A MISS EBOUND. ACR Y CLRED TO LAND RWY 13L. NEXT XMISSION IS TO ACR X TURN R HDG 130 MAINTAIN 2000. ACR Y READS BACK THE HDG R 130 AND ADVISES HE IS ON THE GO. I INSTRUCT ACR Y NEGATIVE FLY HDG 040 (NO ALT). NEXT XMISSION IS TO ACR X R 130 MAINTAIN 2000; WHICH IS READ BACK BY ACR X. I THEN INSTRUCT ACR Y TURN R HDG 130 MAINTAIN 2000. ACR Y DOES NOT ACKNOWLEDGE. AT THIS TIME; BOTH DATA BLOCKS ARE IN THE 10 O'CLOCK POS. ACR X TAG IS COVERING ACR Y ALT AND GNDSPD. AS ACR X TURNS SE; ACR Y ALT IS EXPOSED SHOWING 3000. I SAW DEP WDB FROM LGA (8 MI N OF JFK) CLBING OUT OF 2600. I ISSUED ACR Y TURN R IMMEDIATELY HDG 130 MAINTAIN 2000; TFC 10 O'CLOCK; 2 MI SBOUND. ACR Y READS BACK 130 MAINTAIN 3000. I INSTRUCT ACR Y NEGATIVE; MAINTAIN 2000; WHICH HE READS BACK. THE LGA WDB CAME WITHIN 1 MI AND 100 FT OF ACR Y. THAT NIGHT THE INCIDENT WAS CLASSIFIED A PLTDEV; BUT REVIEW THE FOLLOWING DAY WAS OVERTURNED TO AN OPDEV ON MY PART BECAUSE ACR Y DID NOT READ BACK INSTRUCTIONS OF 130 MAINTAIN 2000.