The problem is that the code is getting executed twice on upload. When the upload is complete, the sketch starts. About 150-180 milliseconds later, Serial Monitor sees that avrdude has disconnected from the Arduino serial port, making it available. Serial Monitor connects to the serial port which causes the auto-reset to occur. The first 150-180 milliseconds of the sketch runs again and gets a different answer because EEPROM was changed the first time.
That is why I always put "delay(200);" after Serial.begin()