RWY ASSIGNMENT WAS CHANGED ON THE CANUK RNAV ARRIVAL AS AN MD80 SERIES WAS APPROACHING ATL. AFTER THE NEW RWY WAS SELECTED; THE FLT CREW OVERSHOT THE RESTRICTION AT CANUK.

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WE WERE GIVEN A CLRNC TO DSND VIA THE CANUK ARR INTO ATL. THE ARR WAS LOADED INTO THE FMS; THEN CHKED AND VERIFIED CORRECT. THE AUTOPLT WAS ENGAGED AND WAS IN VNAV. WHEN ISSUED THE DSCNT CLRNC 4000 FT WAS DIALED INTO THE ALT ALERT WINDOW. THIS WAS THE LOWEST ALT ON THE DSND VIA PROC. WE WERE DSNDING FROM 14000 FT TO CROSS CANUK AT 12000 FT AND 250 KTS. THE AUTOPLT DID NOT LEVEL OFF AT 12000 FT (12000 WAS SHOWING IN THE FMS AS THE LEVELOFF ALT). AT ABOUT 11400 FT THE CAPT DISENGAGED THE AUTOPLT AND STARTED CORRECTING TO MAINTAIN 12000 FT. APCH ASKED OUR ALT WHILE WE WERE CORRECTING; THEN GAVE US A CLRNC TO MAINTAIN 11000 FT. BEFORE OUR DSCNT STARTED WE WERE TOLD TO EXPECT RWY 10. RWY 9R WAS INITIALLY LOADED INTO THE FMS. ALTHOUGH THIS CHANGE DID NOT IMPACT THE FMS DSCNT; I BELIEVE IT DID RESULT IN BOTH PLTS BEING DISTR WITH BRIEFING AND CHANGING APCH CHARTS DURING A CRITICAL STAGE OF FLT. THERE HAVE BEEN MANY PROBS WITH THE MD80 VNAV DSND VIA WHEN RWY CHANGES THAT ARE LINKED TO THE ARR OCCUR. THIS IS DUE TO CHANGING THE FMS; WHICH WILL DROP THE ENTIRE ARR OUT UNTIL IT IS REENTERED. THE AIRPLANE IS SLOW TO ADAPT TO VNAV CHANGE; WHILE WE ARE IN A TIME CRITICAL EVENT. THIS CAN RESULT IN A LOSS OF SITUATIONAL AWARENESS; AS WELL AS MAKING IT HARD TO COMPLY WITH TIGHT ALT AND AIRSPD RESTRS.