ACFT REPORTED 300' HIGH ON REACHING RCA.

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OUR ACFT DEPARTED FTW FOR PAH. WHILE CLBING EBND WE WERE CLRED TO FL230. UPON LEVELING OFF AT FL230 THE CTLR STATED: 'WE SHOW YOU 500' HIGH.' MY ALTIMETER SHOWED US AT FL230 AND WE INFORMED THE CTLR THAT WE WOULD CHANGE TO OUR #2 TRANSPONDER TO SEE IF CORRECT ALT WAS DISPLAYED. WE ASSUMED IT WAS AS WE HAD NO FURTHER COMMENTS FROM ATC. HOWEVER DURING ANOTHER FLT ATC RPTED IT TO BE 1000' LOWER THAN OUR INDICATED ALT DURING THE CLB. RECENTLY IT HAS SHOWED NO ERROR. THIS ACFT HAS BEEN KNOWN TO HAVE AS MUCH AS A 300' ERROR BTWN THE CAPT'S AND COPLTS ALTIMETER AT HIGHER ALTS. THE MODE C INFO IS SENT FROM EITHER DEPENDING UPON WHICH TRANSPONDER IS SELECTED; SO DEPENDING UPON WHICH INFO IS DISPLAYED THERE CAN BE SOME DEVIATION IN MODE C INFO FROM THE ACFT. THIS ERROR; COMBINED WITH ANY ERROR IN ATC'S EQUIPMENT; CAN COMPOUND THE ERROR; ESPECIALLY WHEN FLYING IN TURB. MY CONCERN IS THE ACCURACY OF THE COMBINED READINGS OF THE EQUIP; AS I HEAR QUITE OFTEN; CTLRS TELLING ACFT THAT THEY SHOW THEM HIGH OR LOW ON MODE C READOUTS. IF OUR EQUIP SHOWS ONE ALT AND ATC SHOWS ANOTHER; THEN WHAT IS THE TRUE ALT OF THE ACFT AND IS THE 1000' SEP SAFE AT THE LOWER ALTS? IF 1 ACFT; FOR EXAMPLE IS 300' HIGH AND 1 IS 300' LOW; IT DOESN'T LEAVE MUCH SPACE WHEN SEP IS 1000'. I WOULD NOT FAVOR DECREASING SEP AT HIGH ALTS TO ACCOMMODATE MORE TFC. AS FOR OUR OCCURRENCE; I HAVE NO EXPLANATION FOR THE DIFFERENCE IN ALT READINGS BTWN OUR ACFT AND ATC'S MODE C DISPLAY AND CAN ONLY GUESS THAT IT IS AN ACCUMULATION OF SMALL ERRORS IN THE EQUIP. I WOULD APPRECIATE ANY INFO THAT YOU MAY HAVE ON ANY OCCURRENCES LIKE THIS. CALLBACK CONVERSATION WITH RPTR REVEALED THE FOLLOWING: MAINT FEELS A PITOT SYS MODIFICATION SHOULD BE MADE; BUT IT IS VERY EXPENSIVE AND WILL PROBABLY NOT BE DONE. THE ACFT IS EQUIPPED WITH AIR DATA COMPUTER BUT THAT DOES NOT SEEM TO BE THE PROB. IS GOING TO CHK FURTHER WITH MAINT AND MAY CALL WITH FURTHER INFO. HAS HAD THE SAME PROB WITH ANOTHER FLT AND SEEMS TO FEEL IT IS PRIMARILY THE #2 TRANSPONDER ALTHOUGH THAT IS NOT INDICATED IN THE RPT. ALL CONDITIONS WERE NO CLOUDS AND A VERY RAPID CLB TO ALT.