FLC DISCOVERS THEIR NAV SYS IS ERRONEOUS BY 62 MI AFTER LEARNING THEY HAVE MISSED A REQUIRED XING ALT.

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FLT WAS FROM MCO TO ATL AT FL350. MCO 3 DBN SINCA 2 ATL. ZTL CLRED US FROM FL350 TO FL230 AND DIRECT TO CANUK INTXN PRIOR TO REACHING DBN ON ARR. WE WERE USING FMS AND SELECTED DIRECT CANUK. THE AUTOPLT TURNED TO THE FIX WHICH WAS IDENTED BOTH ON THE FIX PAGE OF THE FMS AND THE INS WAYPOINT. ALL APPEARED CORRECT. WHEN THE FMS SHOWED APPROX 65 NM FROM CANUK; ZTL CLRED US TO CROSS CANUK AT 12000 FT AND 250 KTS BUT TO MAKE THE ALT FIRST AND THEN THE AIRSPD. THIS CLRNC SEEMED A BIT STRANGE AS WE WERE NOW ABOUT 60 NM FROM CANUK AND AN 11000 FT DSCNT AND SLOW DOWN WOULD NORMALLY REQUIRE ABOUT 40-42 NM. COPLT WAS FLYING AND WE BOTH REMARKED TO EACH OTHER THAT IT WOULD BE EASY TO MAKE THE XING RESTR. HOWEVER; DUE TO THE CTLR'S REQUEST TO MAKE THE ALT FIRST AND THEN AIRSPD; I FELT UNEASY AND DECIDED TO CHK RAW DATA BY TURNING OFF MY VOR AUTO TUNE AND MANUALLY TUNING ATL VORTAC. I WAS TOTALLY SURPRISED TO FIND THAT WE WERE 42 NM SE OF ATL VOR; 2 NM FROM CANUK. AT THAT SAME MOMENT; ZTL CALLED BACK AND TOLD US THAT ATL APCH REQUESTED THAT WE MAKE A R 360 DEG TO CROSS CANUK AT 12000 FT AND 250 KTS. WE COMPLIED AND MADE THE RESTR. MEANWHILE; COPLT ALSO TURNED HIS VOR TO MANUAL AND THE FMS THEN UPDATED TO SHOW US OVER CANUK. I WOULD HAVE NORMALLY ADVISED ATC UNABLE TO MAKE RESTR; BUT IT ALL HAPPENED TOO FAST. ALSO; OBVIOUSLY ATC HAD KEPT US TOO HIGH TO MAKE THE RESTR ANYWAY. I CAN'T EXPLAIN WHY FMS WAS APPROX 50 NM IN ERROR BUT AM WORKING WITH MY COMPANY TO FIND AN EXPLANATION.