B747-400 FLC EXPERIENCES AN ALTDEV ALT EXCURSION AFTER PROGRAMMING A FUTURE ALT CHANGE IN THEIR FMC.

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ON ARR TO SFO FROM SEL; A GOLDEN GATE 3 ARR WAS ISSUED WITH A XING RESTR AT LESTR INTXN; 250 KTS; 11000 FT. JUST PRIOR TO LESTR A FURTHER CLRNC OF LESTR; SFO CROSS SFO AT 11000 FT AND DSND TO 6000 FT; HDG 140 DEGS. AN ALT OF 6000 FT WAS SELECTED ON THE FMC AND THE CLRNC WAS ACKNOWLEDGED. THE ACFT ON AUTOPLT FAILED TO LEVEL AT 11000 FT. AT 10700 FT I ENGAGED ALT HOLD AND STARTED A VERT SPD CLB BACK TO 11000 FT. THE DSCNT RATE AT THE TIME WAS 100-200 FPM. THE FLT CONTINUED WITH NO FURTHER INCIDENT. SUPPLEMENTAL INFO FROM ACN 354877: FLT WAS GIVEN A DSCNT TO 6000 FT AFTER SFO VOR AND A HDG FOR VECTORS 140 DEGS. MOMENTS LATER PLANNED RWY WAS CHANGED TO RWY 28L. I PROCEEDED TO LOAD NEW RWY AND POINTED OUT A SHORTCUT TO 'EXTEND CTRLINE' TO CAPT; AS HE WAS NEW ON EQUIP. AS NEW CHANGE WAS EXECUTED THE CAPT NOTICED THE ACFT HAD ALREADY STARTED A DSCNT. THE DSCNT APPEARED AT FIRST TO BE UNCOMMANDED; BUT 6000 FT WAS SET IN ALT ALERT WINDOW AND DURING THE RWY CHANGE INSTRUCTION TO CDU; IT STARTED DOWN BEFORE PLANNED EXECUTE. BEST TO HAVE BEEN IN FLT LEVEL CHANGE MODE. ALSO BACKUP FO'S DID NOT HEAR 'AFTER SFO' IN DSCNT TO 6000 FT. SO THOUGHT 'ALL WAS WELL' AS DSCNT STARTED WHEN CAPT/FO WERE DISTR WITH RWY CHANGE. SUPPLEMENTAL INFO FROM ACN 354399: PROB AROSE BY SETTING LOWER ALT (6000 FT) IN ALT ALERT WINDOW PRIOR TO ACFT LEVELING AND ALT CAPTURE IN VNAV MODE AT 11000 FT. PROB DISCOVERED BY TCASII ALERT. FMS/GLASS COCKPITS HAVE MANY SUBTLE FEATURES WHICH SOMETIMES CAN MISLEAD AND/OR CONFUSE THE PF.