$(function() {
  
  // nav
  $(".nav a").on("click", function(){
   $(".nav").find(".active").removeClass("active");
   $(this).parent().addClass("active");
});
  // end nav
  
  // velocidad parallax
  var parallax = document.querySelectorAll(".parallaxSecundario"),
      speed = 0.5;

  window.onscroll = function(){
    [].slice.call(parallax).forEach(function(el,i){

      var windowYOffset = window.pageYOffset,
          elBackgrounPos = "0 " + (windowYOffset * speed) + "px";
alert(windowYOffset + " * " + speed);
      alert(elBackgrounPos);
      el.style.backgroundPosition = elBackgrounPos;

    });
  };
  // end velocidad parallax
  
  
  $('a[href*="#"]:not([href="#"])').click(function() {
    if (location.pathname.replace(/^\//,'') == this.pathname.replace(/^\//,'') && location.hostname == this.hostname) {
      var target = $(this.hash);
      target = target.length ? target : $('[name=' + this.hash.slice(1) +']');
      if (target.length) {
        $('html, body').animate({
          scrollTop: target.offset().top
        }, 1000);
        return false;
      }
    }
  });

  // Animación
  var $window           = $(window),
      win_height_padded = $window.height() * 1.1,
      isTouch           = Modernizr.touch;

  if (isTouch) { $('.revealOnScroll').addClass('animated'); }

  $window.on('scroll', revealOnScroll);

  function revealOnScroll() {
    var scrolled = $window.scrollTop(),
        win_height_padded = $window.height() * 1.1;

    // Showed...
    $(".revealOnScroll:not(.animated)").each(function () {
      var $this     = $(this),
          offsetTop = $this.offset().top;

      if (scrolled + win_height_padded > offsetTop) {
        if ($this.data('timeout')) {
          window.setTimeout(function(){
            $this.addClass('animated ' + $this.data('animation'));
          }, parseInt($this.data('timeout'),10));
        } else {
          $this.addClass('animated ' + $this.data('animation'));
        }
      }
    });
    // Hidden...
   $(".revealOnScroll.animated").each(function (index) {
      var $this     = $(this),
          offsetTop = $this.offset().top;
      if (scrolled + win_height_padded < offsetTop) {
        $(this).removeClass('animated fadeInUp flipInX lightSpeedIn')
      }
    });
  }

  revealOnScroll();
});

$(function() {
  
  // nav
  $(".nav a").on("click", function(){
   $(".nav").find(".active").removeClass("active");
   $(this).parent().addClass("active");
});
  // end nav
  
  // velocidad parallax
  var parallax = document.querySelectorAll(".parallaxSecundario"),
      speed = 0.5;

  window.onscroll = function(){
    [].slice.call(parallax).forEach(function(el,i){

      var windowYOffset = window.pageYOffset,
          elBackgrounPos = "0 " + (windowYOffset * speed) + "px";

      alert(elBackgrounPos);
      el.style.backgroundPosition = elBackgrounPos;

    });
  };
  // end velocidad parallax
  
  
  $('a[href*="#"]:not([href="#"])').click(function() {
    if (location.pathname.replace(/^\//,'') == this.pathname.replace(/^\//,'') && location.hostname == this.hostname) {
      var target = $(this.hash);
      target = target.length ? target : $('[name=' + this.hash.slice(1) +']');
      if (target.length) {
        $('html, body').animate({
          scrollTop: target.offset().top
        }, 1000);
        return false;
      }
    }
  });

  // Animación
  var $window           = $(window),
      win_height_padded = $window.height() * 1.1,
      isTouch           = Modernizr.touch;

  if (isTouch) { $('.revealOnScroll').addClass('animated'); }

  $window.on('scroll', revealOnScroll);

  function revealOnScroll() {
    var scrolled = $window.scrollTop(),
        win_height_padded = $window.height() * 1.1;

    // Showed...
    $(".revealOnScroll:not(.animated)").each(function () {
      var $this     = $(this),
          offsetTop = $this.offset().top;

      if (scrolled + win_height_padded > offsetTop) {
        if ($this.data('timeout')) {
          window.setTimeout(function(){
            $this.addClass('animated ' + $this.data('animation'));
          }, parseInt($this.data('timeout'),10));
        } else {
          $this.addClass('animated ' + $this.data('animation'));
        }
      }
    });
    // Hidden...
   $(".revealOnScroll.animated").each(function (index) {
      var $this     = $(this),
          offsetTop = $this.offset().top;
      if (scrolled + win_height_padded < offsetTop) {
        $(this).removeClass('animated fadeInUp flipInX lightSpeedIn')
      }
    });
  }

  revealOnScroll();
});

Update script.js