A B727-200 FLC EXPERIENCES A LOSS OF ALT INFO WHEN THEIR 2 ALTIMETERS DISAGREE WHILE INFLT AT FL250. APCH TO JFK IS DONE IN VMC CONDITIONS.

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FLT FROM MCO TO JFK. PRIOR TO DEP THE CAPT'S ALTIMETER INDICATED 100 FT HIGH IN THE STANDBY MODE. THE STANDBY MODE IS PUT ON MAINT CARRY OVER BY MAINT. NOW WE HAVE THE FO'S ALTIMETER AVAILABLE AND THE CAPT'S ALTIMETER IN CENTRAL AIR DATA COMPUTER MODE. EARLIER IN THE DAY THE CAPT'S ALTIMETER WAS WORKED ON; AND I BELIEVE REPLACED. THE FLT DEPARTS MCO NORMALLY AND CLBS TO FL250; BOTH ALTIMETERS ARE SET TO 29.92 INCHES AT 18000 FT MSL; HOWEVER THE FO'S ALTIMETER IS LAGGING SLIGHTLY BEHIND THE CAPT'S ALTIMETER. INDICATING LEVEL AT FL250 ON THE CAPT'S ALTIMETER AND SLIGHTLY LOWER (MAYBE 100-150 FT) ON THE FO'S ALTIMETER; THE FO ASKS ATC WHAT ALT ATC SHOWS THE FLT ON THEIR RADAR. ATC REPLIES LEVEL AT FL250. WE COMPLETE THE APPROPRIATE CHKLIST FOR UNRELIABLE ALT INDICATIONS; AND SUSPECT THE FO'S ALTIMETER OF THE MALFUNCTION. THE CHKLIST CALLS FOR USING THE LOWEST INDICATED ALT; HOWEVER AS A CREW; WE DECIDED TO USE THE CAPT'S ALTIMETER; ALTHOUGH HIGHER; IT WAS IN AGREEMENT WITH ATC'S READOUT FROM OUR XPONDER. FURTHER ALONG IN THE FLT THE FO'S ALTIMETER STARTS DSNDING AT A RATE OF APPROX 10 FPM. AT APPROX 150 NM S OF NORFOLK; VA; THE FO'S ALTIMETER IS ABOUT 600 FT LOW AND STILL DSNDING. APPROX 20 MINS LATER; IN LEVEL FLT; THE CAPT'S ALTIMETER ROLLS RAPIDLY (LESS THAN 2 SECONDS) TO SHOW AN INDICATED ALT OF APPROX 24000 FT MSL. WE NOTIFIED ATC OF THE SIT AND THAT WE WERE UNABLE TO VERIFY OUR ALT. ATC REPLIED THEY STILL SHOWED US LEVEL AT FL250. WE TOLD ATC THAT THEY SHOULD BE SUSPICIOUS OF ANY ALT READOUTS RECEIVED FROM OUR ACFT. ATC REPLIED THEY UNDERSTOOD AND WOULD NOT CLR ANY ACFT WITHIN 2000 FT OF OUR FLT PATH. THE WX AT JFK WAS RPTED AS GOOD VFR SO WE AS A CREW DECIDED TO PROCEED TO OUR DEST. ON LEVELOFF DURING OUR DSCNT ATC GENERALLY SHOWED US APPROX 1000 FT OFF WHAT WE WERE INDICATING AND ASKED US TO TURN OFF OUR ALT RPTING; BUT WE ELECTED TO LEAVE IT ON TO GET SOME INFO FROM THE TCASII. THE FLT COMPLETED THE VOR RWY 13L APCH AND LANDED RWY 13R AT JFK. DURING THE APCH THE FO'S ALTIMETER WAS INDICATING CLOSER THAN THE CAPT'S TO THE RADAR ALTIMETER (TERRAIN APPROX SEA LEVEL). I CALLED MAINT THE NEXT DAY AND WAS TOLD THE CAPT'S CADC FAILED AND THE FO'S ALTIMETER FAILED. MY HYPOTHESIS TO THIS SIT IS THAT THE PROB WAS CREATED EARLIER IN THE DAY; PRIOR TO THE FLT; WHEN THE SYS WAS WORKED ON BY MAINT; EITHER BY FAULTY PARTS; INCORRECT INSTALLATION; OR BOTH. ONE POSSIBLE PIECE OF EQUIP THAT COULD HAVE HELPED IN THIS SIT WOULD HAVE BEEN GPS.