Arduino 1.6.9 uses 13 instead of LED_BUILTIN, which is equal to 7 in the newest version. Writing to the wrong port causes the wrong result.

Full code

Arduino 1.6.9

/*
  Blink
  Turns on an LED on for one second, then off for one second, repeatedly.

  Most Arduinos have an on-board LED you can control. On the Uno and
  Leonardo, it is attached to digital pin 13. If you're unsure what
  pin the on-board LED is connected to on your Arduino model, check
  the documentation at http://www.arduino.cc

  This example code is in the public domain.

  modified 8 May 2014
  by Scott Fitzgerald
 */


// the setup function runs once when you press reset or power the board
void setup() {
  // initialize digital pin 13 as an output.
  Serial.begin(9600);
  pinMode(13, OUTPUT);
}

// the loop function runs over and over again forever
void loop() {
  Serial.println(13);
  digitalWrite(13, HIGH);   // turn the LED on (HIGH is the voltage level)
  delay(1000);              // wait for a second
  digitalWrite(13, LOW);    // turn the LED off by making the voltage LOW
  delay(1000);              // wait for a second
}

Arduino 1.8.8

/*
  Blink

  Turns an LED on for one second, then off for one second, repeatedly.

  Most Arduinos have an on-board LED you can control. On the UNO, MEGA and ZERO
  it is attached to digital pin 13, on MKR1000 on pin 6. LED_BUILTIN is set to
  the correct LED pin independent of which board is used.
  If you want to know what pin the on-board LED is connected to on your Arduino
  model, check the Technical Specs of your board at:
  https://www.arduino.cc/en/Main/Products

  modified 8 May 2014
  by Scott Fitzgerald
  modified 2 Sep 2016
  by Arturo Guadalupi
  modified 8 Sep 2016
  by Colby Newman

  This example code is in the public domain.

  http://www.arduino.cc/en/Tutorial/Blink
*/

// the setup function runs once when you press reset or power the board
void setup() {
  // initialize digital pin LED_BUILTIN as an output.
  pinMode(LED_BUILTIN, OUTPUT);
}

// the loop function runs over and over again forever
void loop() {
  digitalWrite(LED_BUILTIN, HIGH);   // turn the LED on (HIGH is the voltage level)
  delay(1000);                       // wait for a second
  digitalWrite(LED_BUILTIN, LOW);    // turn the LED off by making the voltage LOW
  delay(1000);                       // wait for a second
}

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