I have been using the same micro: AT89S8252. Sometimes (not very often) it destroys data in eeprom memory. Sometimes 1, sometimes 3 bytes - I don't know the rule. ATMEL has published an errata for AT89S/LS8252 at its web site. About two weeks ago I sent it to local ATMEL's office and they didn't answer me yet. ATMEL is writing about revision "T" of micro, but how recognize this?
My application is good, I think. I have been using voltage supervisory (TL7705), output/input drivers etc. It does not matter what is your applicatin in this case. ATMEL make mistake during manufacturing the micro, I think. You should contact the local ATMEL's office/distributor.
I have never heard about these problems with another ATMEL's micro. Maybe you should to change it? If it is medical equipment, maybe using an external eeprom to store data is better solution?