FLC OF AN LTT FLEW WRONG FL PLAN ROUTING DUE TO ANOTHER STOP PUT INTO THE NORMAL SCHEDULED FLT THAT WAS DIFFERENT FROM THAT OF THE STORED FLT PLAN.

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DURING A ROUND TRIP FROM BOS-ISP-BOS; WE WERE TOLD TO MAKE A FLAG STOP IN BDR AFTER STOPPING IN ISP. WHEN TRYING TO PICK UP OUR CLRNC FROM ISP TWR; WE WERE TOLD THAT AN IFR CLRNC COULD NOT BE FOUND ON FILE. ISP TWR PUT IN A CLRNC FOR US. DEPARTING BDR; WE WERE TOLD BY BDR TWR THAT ONCE AGAIN; NO CLRNC WAS ON FILE. THEY TOLD US THEY HAD A CLRNC FOR THE PREVIOUS FLT WHICH HAD CANCELED. BDR OPS TOLD US THAT WE COULD USE THAT CLRNC. BDR TWR READ THE CLRNC AS 'CLRED TO BOS VIA BRIDGEHAVEN 5 DEP; MADISON; AS FILED' WITH 13000 FT AS A FINAL ALT WHICH SEEMED TO GO WITH OUR PAPER WORK WHICH SHOWED US FILED MAD V1 HFD THEN DREEM INTXN; DIRECT BOSTON. CLBING OVER MAD VOR ON OUR DEP; WE TURNED TO TRACK V1 TO HFD. APPROX 8 MI N OF MADISON; NEW YORK ASKED US TO VERIFY OUR RTE AND TOLD US THAT WE SHOULD BE ON VICTOR 475 TO ORW WITH 9000 FT AS OUR FINAL. THIS MIX-UP MAY BE DUE TO THE 2 FLT PLANS BEING FILED DIFFERENTLY; HOWEVER; THEY HAVE ALWAYS BEEN THE SAME IN THE PAST AS THEY ARE COMPUTER GENERATED 'CANNED' FLT PLANS. ALSO; THE FACT THAT WE WERE GIVEN 13000 FT AS A FINAL WOULD KEEP US AWAY FROM THE V-475 RTE TO ORW; THEN V-16 WOONS TO BOSTON. THESE CONFLICTS MAY HAVE COME TO ME SOONER HAD IT NOT BEEN THE 8TH LEG OF OUR DAY.