UPON INITIAL CONTACT WITH ZNY ARTCC AN ACR B737 COPIED A CLRNC TO GO DIRECT RBV AND CLB TO 15000 FT. THIS WAS NOT ON THE B737'S RTE OF FLT AND THEY QUESTIONED THE CLRNC. THE B737 RECEIVED A TCASII ALERT ON AN ACR B727 DSNDING AND AT THAT TIME THE CTLR TOLD THEM TO MAINTAIN 9000 FT AND PROCEED DIRECT COL DIRECT WHITE AS FILED. SEPARATION WAS LOST; BUT THE B737 DID HAVE VISUAL CONTACT WITH THE B727 AS IT WAS RESPONDING TO A TCASII RA. ACFT MISSED BY 1 MI AND 600 FT.

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XA10L EDT UNEVENTFUL TKOF OUT OF EWR HDG FOR MCO. FLEW THE ARTHUR KILL SID AND SWITCHED TO DEP CTL. DEP TOLD US TO INTERCEPT THE 350 DEG RADIAL INTO COL AND MAINTAIN 6000 FT THEN SWITCHED US TO FREQ 124.75. WE CHKED ON AND WERE TOLD TO CLB TO 15000 FT AND GO DIRECT TO RBV. WE IMMEDIATELY QUESTIONED THE DIRECT RBV PART AND ASKED THE CTLR IF SHE WAS SURE SHE WANTED US TO GO DIRECT RBV BECAUSE IT WASN'T ON OUR RTE OF FLT. WE WERE TOLD TO 'STANDBY.' MEANWHILE WE HAD BEGUN OUR CLBOUT OF 6000 FT AND WERE AT APPROX 9200 FT WHEN WE HAD A TCASII TA AND WE SAW THE TFC AT 12 O'CLOCK; 9600 FT. WE THEN RECEIVED A TCASII ADVISORY TO DSND; WHICH WE DID. WHILE ALL THIS WAS HAPPENING THE CTLR ASKED US WHAT ALT WE WERE CLBING TO AND WE ANSWERED; '15000 FT ASSIGNED.' SHE SAID 'NEGATIVE' AND WE TOLD HER WE WERE TOLD TO 'CLB TO 15000 FT AND GO DIRECT RBV.' SHE ANSWERED 'NEGATIVE.' SHE THEN TOLD US TO MAINTAIN OUR PRESENT ALT. WE WERE AT 9000 FT. THEN WE WERE TOLD TO GO DIRECT COL DIRECT WHITE AS FILED. THE CTLR WAS EXTREMELY BUSY WITH US AND NUMEROUS OTHER AIRPLANES SHE WAS CTLING. FROM THE FIRST TCASII ALERT WE HAD THE OTHER AIRPLANE IN SIGHT AND THE EVASIVE ACTION TAKEN WAS VERY SMOOTH AND NOT NOTICEABLE TO ANYONE ELSE IN THE AIRPLANE. THE OTHER ACFT PASSED OFF TO THE L AND APPROX 500 FT HIGHER IN ALT AND 1 MI HORIZ. WE KNOW WE WERE TOLD 'CLB TO 15000 FT AND GO DIRECT RBV.' WE ACKNOWLEDGED THAT CLRNC AND READ IT BACK.