BE9L HAS LOSS OF SEPARATION WITH SAAB 340 10000 FT OVER CHOPPY DUE TO CTLR ERROR.

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S OF CHOPPY INTXN; FLYING DIRECT TO LFV; CLBING IN IMC TO 11000 FT; AT APPROX 9700 FT; WE RECEIVED A TCAS TA. I SWITCHED THE TCAS DISPLAY TO 2 NM AND LOCATED THE TFC AT 1-2 O'CLOCK POS; DSNDING; LESS THAN 1 MI; WITH 700 FT SEPARATION. THE PF DISCONNECTED THE AUTOPLT AND INITIATED A TURN TO THE L AS THE TFC PASSED AFT OF THE R WING WITH 300 FT SEPARATION AND LESS THAN 1/2 MI. WE WERE CLBING TO 10000 FT WITH CAPE APCH; AND THEN HANDED OFF TO ZBW (128.75) AND INSTRUCTED TO CLB TO 11000 FT. I ASKED BOS IF HE WAS WORKING THE TFC THAT JUST PASSED OFF OUR R WING AND THE CTLR SAID THE ACFT WAS WORKING CAPE APCH. I TOLD HIM OF THE LOSS OF SEPARATION AND THAT I WOULD BE FILING A 'NEAR MISS' RPT. 10-15 MINS LATER JUST PRIOR TO HDOF; THE SAME CTLR ADVISED THAT THEY WERE LOOKING INTO THE SITUATION AND THAT I COULD CALL FOR INFO IN ABOUT AN HR. AFTER RETURNING TO BTV I CONTACTED ZBW AND WAS ADVISED THAT THE LOSS OF SEPARATION WAS THE FAULT OF THE CAPE APCH/DEP CTLR WHO 'LOST TRACK' OF THE SITUATION. HE WAS CTLING ACFT Y OVERFLT FROM ACK TO LGA. HE PREMATURELY CLBED US TO 10000 FT AND MADE THE HDOF TO BOS WITHOUT PROPERLY ASSESSING THE CONFLICT POSSIBILITY. HE STATED THAT THE SEPARATION WAS REDUCED TO 3/10 MI LATERAL AND 500 FT VERT. I INQUIRED AS TO WHY THE BOS CTLR DIDN'T PICK UP ON THE SITUATION; AND WHY DIDN'T THE CONFLICT ALERT SYS WORK. HE EXPLAINED THAT THE RADAR RETURN FROM THE CAPE CTLED ACFT WOULD NOT HAVE HAD A 'DATA BLOCK' BUT ONLY A PRIMARY TARGET. ALSO THERE WAS A VERY HVY TFC SITUATION IN PROGRESS AND THE PRIMARY TARGET MAY HAVE BEEN COMBINED WITH OTHER TFC ABOVE OR BELOW. AS FOR THE CONFLICT ALERT SYS HE SAID IT IS OFTEN UNRELIABLE FOR MANY REASONS; ONE OF WHICH IS MISSED MODE-C (SKIPPED) DATA.