DUE TO FAULTY MAP ALIGNMENT OF FMC DISPLAY ACR WDB INCURRED TRACK DEVIATION ON DEP.

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TOOK OFF FROM JFK RWY 31L ON A 'KENNEDY 1 DEP; BREEZY POINT CLB.' AT 400' WE TURNED LEFT TO PROCEED TO CRI VOR. (RPTR FLYING AS SUPVR IN RIGHT SEAT PERFORMING F/O DUTIES.) WHEN TURN TOWARDS CRI VOR WAS INITIATED; I SELECTED A 'DIRECT TO CRI IN FMC; CDU.' WHEN THIS WAS EXECUTED CAPT FLYING FOLLOWED COMMAND BARS TO FLY TO CRI WHICH NOW SHOWED STRAIGHT AHEAD ON OUR HSI'S. CTLR ASKED WHERE WE WERE HDG (KENNEDY DEP 135.9). HE ADVISED THAT CRI WAS TO OUR 9 O'CLOCK AND GAVE US A LEFT TURN TO 220 DEGS VECTOR. AS WE TURNED AS DIRECTED; THE MAP ON OUR HSI'S SHIFTED AND CRI VOR NOW SHOWED ACCURATELY. THE POS ERROR CAUSED BY THIS MAP SHIFT WAS SIGNIFICANT ENOUGH TO REQUIRE A VECTOR. WE HAD TAXIED IN HEAVY GND TFC AT JFK FOR 40 MINS SINCE ALIGNMENT OF THE HSI'S. IN THE FUTURE; I INTEND TO HAVE 1 PLT IN VOR MODE ON HSI WITH VOR MANUALLY SELECTED TO ABSOLUTELY VERIFY THE ACCURACY OF DEP ROUTING. THE REST OF THE FLT WAS ROUTINE AND AT THE END OF A 6 HR FLT TO SAN; THE HSI ACCURACY CHK WAS RIGHT ON THE MONEY AND THE FMC'S WERE ALSO RIGHT ON. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING: HSI UNITS WERE ALIGNED AT GATE AND CAME UP PROPERLY. TAXI TO RWY WAS EXTENSIVE AND MUCH DELAY; 40 MINS BLOCK TO TKOF. ONE VOR NAVAID WAS IN THE MANUAL MODE AND TURNED TO CRI FOR BACK UP ON DEP. NORMALLY THEY ARE IN AUTO MODE FOR FMC UPDATING OF POS. IT SHOULD HAVE BEEN WORKING ON GND EVEN IN THIS CONDITION; BUT SOMETIMES WITH NUMEROUS ACFT AROUND THE ACFT CANNOT RECEIVE VOR DME SIGNALS ON THE GND AND THUS UPDATE THE FMC POS. RPTR TALKED TO MFG TECH REP AND HE STATED THAT IN EUROPE THIS PROB HAS HAPPENED AND CONSEQUENTLY SOME OPERATORS THERE ARE NOW HAVING ONE SET OF FLT INSTRUMENTS IN THE VOR MODE FOR DEPS TO ASSURE POS UNTIL AIRBORNE LONG ENOUGH TO VERIFY THE FMC POS IS ACCURATE.