AN ACR MLG FLC CLBED ABOVE THEIR CLRED ALT. THE FLC SUSPECTS A MALFUNCTION IN THE AUTOFLT GUIDANCE SYS; BUT COULD NOT VERIFY THIS. THE SYS OPERATED PERFECTLY FOR THE REMAINDER OF THE FLT.

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ATC CLRNC 'CLB TO 6000 FT MSL; L TURN 220 DEGS TO INTERCEPT COL 350 DEG RADIAL.' AS PNF; I DIVERTED ATTN TO FMC TO SET UP COURSE INTERCEPT FOR PF. HE WAS FLYING MANUALLY. I HAD SET 6000 FT IN ALT WINDOW AND THEN BEGAN TO SET UP COURSE INTERCEPT. FOR SOME UNKNOWN REASON; I HAD TO REPEAT THE SETUP AND WHILE ATTEMPTING SECOND TIME; PF QUERIED '6000 FT?' I LOOKED UP AND CONFIRMED '6000 FT' AND NOTICED WE WERE LEVELING AT 7000 FT MSL. PF BEGAN IMMEDIATE CORRECTION TO 6000 FT AND STATED THAT THE COMMAND BARS INDICATED CLB UNTIL HE FINALLY QUERIED '6000 FT?' AS WE APCHED 7000 FT MSL. WE HAVE NO EXPLANATION WHY COMMAND BARS COMMANDED CLB. HE ALSO STATED; AUTOTHROTTLES DID NOT RETARD. HIS CORRECTION BACK TO 6000 FT WAS IMMEDIATE. UPON REACHING 6000 FT; DEP CLRED US TO HIGHER (I THINK 12000 FT) AND WE BEGAN CLB. PASSING 6400 FT ATC REQUESTED OUR ALT AND WE RESPONDED 6400 FT CLBING TO 12000 FT. ATC SAID NOTHING FURTHER; NOR DID WE. MISTAKES: 1) PNF DIVERTED ATTN TO FMC TOO LONG AT ONE TIME. 2) PF DIDN'T MONITOR ALTIMETER AS WELL AS COMMAND BARS. IF ALT WARNING AND AUTOTHROTTLES MALFUNCTIONED; IT NEVER HAPPENED AGAIN FOR ENTIRE FLT (NO EXPLANATION). WE WONDER IF SAME WOULD HAVE OCCURRED WITH AUTOPLT FLYING.