Smooth scrolling end positioning

Question

I have a nifty smooth animated scroll that goes up and down depending on what you click on the navigation (thanks to CSS-Tricks!). Now this is all working great but I have a nav that sticks to the top of the browser window and gets in the way of the section headers when it scrolls down. I can't for the life of me find anyone who may have had a similar issue with, what seems like, a very simple function.

Here's the JS that I have pasted into my HTML:

<script type="text/javascript">
$(document).ready(function() {
  function filterPath(string) {
  return string
    .replace(/^\//,'')
    .replace(/(index|default).[a-zA-Z]{3,4}$/,'')
    .replace(/\/$/,'');
  }
  var locationPath = filterPath(location.pathname);
  var scrollElem = scrollableElement('html', 'body');

   $('a[href*=#]').each(function() {
    var thisPath = filterPath(this.pathname) || locationPath;
    if (  locationPath == thisPath
    && (location.hostname == this.hostname || !this.hostname)
    && this.hash.replace(/#/,'') ) {
      var $target = $(this.hash), target = this.hash;
      if (target) {
        var targetOffset = $target.offset().top;
        $(this).click(function(event) {
          event.preventDefault();
          $(scrollElem).animate({scrollTop: targetOffset}, 800, function() {
            location.hash = target;
          });
        });
      }
    }
  });

  // use the first element that is "scrollable"
  function scrollableElement(els) {
    for (var i = 0, argLength = arguments.length; i <argLength; i++) {
      var el = arguments[i],
          $scrollElement = $(el);
      if ($scrollElement.scrollTop()> 0) {
         return el;
      } else {
        $scrollElement.scrollTop(1);
        var isScrollable = $scrollElement.scrollTop()> 0;
        $scrollElement.scrollTop(0);
        if (isScrollable) {
          return el;
        }
      }
    }
    return [];
  }

});</script>

So I am in the process of learning JS and JQuery so I appreciate everyones patience and look forward to hearing your comments.

Many thanks in advance.

Edit: here is my test site: test