For the record, this is what I was talking about (I'm an idiot):
Yeah if anything, changing the settings in code itself - you'll probably also need to change the memory settings value that checks if the stored eeprom matches the config. Think its called version or something. Without changing that to something else too, arduinoboy wont reload the settings into eeprom. Which is probably what you were experiencing.
Guess I'll have to figure out this version/memory setting.