I would like to understand what has been written to the EEPROM in a failed condition. Can you provide a dump of EEPROM contents when the failure happens? If you are not writing during power down the situation of corruption of EEPROM during power down is unlikely.
Glitches usually cannot happen to complete a write. The other thing I would suspect is on power up, if the bootloader is writing some contents to EEPROM. The dump of EEPROM values can help analyze the failure better. This may involve further debug, I suggest we create a case and continue more step by step debug. Can you create a tech support case and we can take it further.