BOTH PLTS INPUT INFO TO THE AUTOPLT AND ONE CANCELLED THE OTHER RESULTING IN CLBING ABOVE ASSIGNED ALT.

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IN CRUISE FLT AT 16000 FT WE WERE GIVEN A REVISED ALTIMETER SETTING WHICH CAUSED A SIGNIFICANT CHANGE IN INDICATED ALT. WE WERE ALSO GIVEN A DSCNT CLRNC IN THE FORM OF A XING RESTR. THE PF COMMANDED HIS FLT DIRECTOR TO 'CLB' IN AN EFFORT TO CORRECT THE INDICATED ALT CHANGE CAUSED BY THE NEW ALTIMETER SETTING. THE AUTOPLT FOLLOWED THIS COMMAND; HOWEVER; THE PNF HAD SET THE ALT GIVEN IN THE DSCNT CLRNC IN THE ALT PRE-SELECTOR. THIS ACTION REMOVED THE ALT REF FOR THE AUTOPLT 'CLB' FUNCTION. CONCURRENT TO THESE EVENTS; BOTH PLTS BECAME DISTR DISCUSSING A PLAN TO DEVIATE AROUND PRECIP BEING DEPICTED BY RADAR. DUE TO THE IMPROPER AUTOPLT INPUT THE AIRPLANE DEVIATED VERTLY (CLBED ABOVE) FROM THE ASSIGNED ALT. UPON NOTICING THE DEV WE DISCONNECTED THE AUTOPLT AND MANUALLY FLEW THE AIRPLANE BACK TO THE CORRECT ALT. AFTER THE SIT WAS CORRECT WE QUERIED THE CTLR; RPTING OUR DEV AND ASKING IF THIS HAD CAUSED ANY PROB. HE REPLIED IT DID NOT. BETTER COCKPIT COMS AND DIVISION OF TASKS; WITH REGARD TO THE RADAR DISTR; WOULD HAVE PREVENTED THIS EVENT.