I am trying to use this example(it works on arduino mega): millis() - lowIn comes greater than 5000when motion ends

/////////////////////////////
//VARS
//the time we give the sensor to calibrate (10-60 secs according to the datasheet)
int calibrationTime = 30;

//the time when the sensor outputs a low impulse
long unsigned int lowIn;

//the amount of milliseconds the sensor has to be low
//before we assume all motion has stopped
long unsigned int pause = 5000;

boolean lockLow = true;
boolean takeLowTime;

int pirPin = 3;    //the digital pin connected to the PIR sensor's output
int ledPin = 13;


/////////////////////////////
//SETUP
void setup() {
  Serial.begin(9600);
  pinMode(pirPin, INPUT);
  pinMode(ledPin, OUTPUT);
  digitalWrite(pirPin, LOW);

  //give the sensor some time to calibrate
  Serial.print("calibrating sensor ");
  for (int i = 0; i < calibrationTime; i++) {
    Serial.print(".");
    delay(1000);
  }
  Serial.println(" done");
  Serial.println("SENSOR ACTIVE");
  delay(50);
}

////////////////////////////
//LOOP
void loop() {

  if (digitalRead(pirPin) == HIGH) {
    digitalWrite(ledPin, HIGH);   //the led visualizes the sensors output pin state
    if (lockLow) {
      //makes sure we wait for a transition to LOW before any further output is made:
      lockLow = false;
      Serial.println("---");
      Serial.print("motion detected at ");
      Serial.print(millis() / 1000);
      Serial.println(" sec");
      delay(50);
    }
    takeLowTime = true;
  }

  if (digitalRead(pirPin) == LOW) {
    digitalWrite(ledPin, LOW);  //the led visualizes the sensors output pin state

    if (takeLowTime) {
      lowIn = millis();          //save the time of the transition from high to LOW
      takeLowTime = false;       //make sure this is only done at the start of a LOW phase
    }
    //if the sensor is low for more than the given pause,
    //we assume that no more motion is going to happen
    Serial.print(millis() - lowIn);
    Serial.print("    ");
    Serial.print(lockLow);
    Serial.print("    ");
    Serial.println(pause);
    if (!lockLow && millis() - lowIn > pause) {
      //makes sure this block of code is only executed again after
      //a new motion sequence has been detected
      lockLow = true;
      Serial.print("motion ended at ");      //output
      Serial.print((millis() - pause) / 1000);
      Serial.println(" sec");
      delay(50);
    }
  }
}

but it doesnt work on yun shield mounted on Arduino Leonardo. the difference of millis() - lowIn always comes out to be lower than pause.