Issue with StandardFirmata and Arduino Mega 2560

Projects Interfacing w/ Software on the Computer
6 
  arduino.pinMode(SPACE_PIN, Arduino.OUTPUT);
  arduino.pinMode(SPACE_PIN2, Arduino.OUTPUT);
  arduino.pinMode(SPACE_PIN3, Arduino.OUTPUT);
  arduino.pinMode(SPACE_PIN4, Arduino.OUTPUT);
  arduino.pinMode(SPACE_PIN5, Arduino.OUTPUT);
  arduino.pinMode(SPACEREDLED_PIN, Arduino.OUTPUT);

This is setting the mode in the arduino instance, which passed that information on the Arduino, when needed. You are not defining the ANALOG pins as analog pins to the arduino instance. The Arduino already knows that they are analog pins, but the arduino instance does not.