The subject line pretty much says it all. I'm certain I am programming the EEPROM (and not registers or RAM, which are located well away from the EEPROM). I can see the EEPROM data either with the Cyclone Pro, or else via a serial port command to dump the EEPROM (used when Cyclone Pro is disconnected). While my program is running, the EEPROM data changes only in response to a user command; it is never changed autonomously by the program. But when I cycle power, whatever data is there has been replaced by garbage. The garbage is always the same for a given board, but is different for various boards.
I suppose I should add that I am using CodeWarrior and Processor Expert, but I don't see what that would have to do with it.