They said there are two flash units with the same image and on each reboot it tried the opposite image. So the odds it’s the flash memory is low. They said there are a couple common interface chips that could be the problem. Maybe a stuck address line or something. Or it might just be software.

Flash memory is used on military and space applications often. However, usually the flash is used for non-critical data and the OS is loaded from ROM. It sounds like they use the EEPROM on spirit for some critical updates to flight software. Flash is mainly used for science data and for storing command data overnight.