FLC OF A CPR B727 FAILED TO FOLLOW ASSIGNED TRACK DURING CLB DUE TO NOT REPROGRAMMING THE FMS WITH THE ACTUAL CLRNC GIVEN IN THEIR PDC.

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TRIP WAS PLANNED AS A CRP PAX DROP-OFF/QUICK TURN IN PHL CONTINUING TO SWF. WHILE I WAS ASSISTING THE PAX TO THEIR TRANSPORTATION; THE CO-CAPT RECEIVED ATC CLRNC VIA PDC. I HAD VERBALLY FILED A FLT PLAN WITH FSS WITH A ROUTING WE HAD PREVIOUSLY FLOWN AND STORED IN THE FMS: DITCH; V312; CYN; JFK; DPK; MAD; MAD341; BRISS; PHL; V433; TRESA; SWF. THE CO-CAPT LOADED THAT FLT PLAN INTO BOTH FMS'S. THE PDC WAS THE SAME ROUTING AS FILED EXCEPT FOR THE INITIAL AIRWAY. WHEN I RETURNED TO THE COCKPIT I REVIEWED THE PDC ON THE FMS AND WAS SURPRISED TO SEE 'AS FILED' SINCE THE ROUTING ALMOST ALWAYS CHANGES. WE BOTH MISSED THE CHANGE TO THE INITIAL PORTION OF THE CLRNC: DITCH J225 JFK AS FILED. AFTER TKOF; WE WERE GIVEN VECTORS IN THE GENERAL DIRECTION OF DITCH; THEN CLRED DIRECT. AFTER PASSING DITCH; STILL CLBING TO FL290 WE WERE PROCEEDING TO CYN WHEN THE CTLR GAVE US A HDG OF 010 DEGS TO INTERCEPT J225. AS WE WERE NOT PREPARED FOR THE FIX/RADIAL OF THAT AIRWAY; WE LOOKED AT THE UNITED STATES HIGH CHART AND HAD A GREAT DEAL OF TROUBLE LOCATING THE AIRWAY. IN THAT AREA; J225 BEGINS AT VCN; AND THE IDENT FOR THAT AIRWAY ON THE CHART WAS FAR S OF OUR PRESENT LOCATION. BY THE TIME WE LOCATED THE AIRWAY AND WERE TUNING THE RADIOS; WE WERE PROBABLY THROUGH THE RTE. THE CTLR (ZNY) ASKED US 'IF WE EVEN KNEW WHERE J225 WAS' AND TOLD US TO PROCEED DIRECT TO DPK. I BELIEVE THAT WE MISSED THE J225 READOUT ON THE PDC DUE TO THE WAY IT WAS PRESENTED ON THE FMS. DITCH WAS THERE AS WAS JFK AND AS FILED; HOWEVER; THE SENTENCE BREAK ON THE FMS WAS SUCH THAT J225 WAS MISSED. IF WE HAD RECEIVED THE CLRNC VIA RADIO IT WOULD HAVE BEEN WRITTEN DOWN AND THE FMS REPROGRAMMED FOR THE CORRECT ROUTING TO JFK. CONTRIBUTING TO THIS WAS MY ABSENCE FROM THE COCKPIT WHILE THE FMS WAS PROGRAMMED AND RELIANCE ON THE AS FILED STATEMENT IN THE CLRNC. WHILE WE DO NOT THINK WE VIOLATED ANY REG; IMPROPER PROGRAMMING OF FMS/EFIS EQUIPPED ACFT SEEMS TO BE A RECURRING PROB AREA; AS BROUGHT OUT IN SEVERAL ASRS RPTS. WE HAVE REVIEWED OUR CLRNC DELIVERY PROCS AS THEY APPLY TO THE AFIS PDC SYS AS WELL AS OUR FMS PROGRAMMING. ONE PLT WILL LOAD AND COMPARE THE FLT PLAN WITH THE ONE RECEIVED VIA AFIS; THE OTHER WILL LOAD THE FLT PLAN RECEIVED BY CLRNC DELIVERY (OR PDC). THE FLT PLAN FROM PDC WILL BE DISPLAYED VIA THE 'CLRNC' READOUT ON THE FMS AND BOTH WILL BE COMPARED ON THE MULTI-FUNCTION DISPLAY. IN THIS MANNER; RELIANCE ON OUR STORED 'PLT RTES' THAT DIFFER FROM OUR CLRNC WILL BE READILY IDENTED.