Hi,
Sorry for the delay.
Here is your code working as desired. Have a look at what I have done and let me know if you have any questions.
<!DOCTYPE html>
<html lang="en">
<head>
<base href="http://designpencil.com/" />
<meta charset="utf-8">
<title>Flexslider in Modal</title>
<link href="css/bootstrap.min.css" rel="stylesheet">
<link href="css/full-slider.css" rel="stylesheet">
<link rel="stylesheet" href="css/flexslider.css" type="text/css" media="screen" />
</head>
<body>
<section id="portfolio" class="bg-light-gray">
<div class="container">
<div class="row">
<div class="col-md-4 col-sm-6 portfolio-item">
<a href="#" class="portfolio-link" data-toggle="modal" data-target="#lightbox" data-slide-to="0">
<img src="http://placehold.it/400x200/red" class="img-responsive" alt="">
</a>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<a href="#" class="portfolio-link" data-toggle="modal" data-target="#lightbox" data-slide-to="1" >
<img src="http://placehold.it/400x200/red" class="img-responsive" alt="" >
</a>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<a href="#" class="portfolio-link" data-toggle="modal" data-target="#lightbox" data-slide-to="2">
<img src="http://placehold.it/400x200/777" class="img-responsive" alt="">
</a>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<a href="#" class="portfolio-link" data-toggle="modal" data-target="#lightbox" data-slide-to="3">
<img src="http://placehold.it/400x200/999" class="img-responsive" alt="">
</a>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<a href="#" class="portfolio-link" data-toggle="modal" data-target="#lightbox" data-slide-to="4">
<img src="http://placehold.it/400x200/blue" class="img-responsive" alt="">
</a>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<a href="#" class="portfolio-link" data-toggle="modal" data-target="#lightbox" data-slide-to="5">
<img src="http://placehold.it/400x200/yellow" class="img-responsive" alt="">
</a>
</div>
</div>
</div>
</section>
<div id="lightbox" class="portfolio-modal modal fade " role="dialog" aria-labelledby="gridSystemModalLabel" aria-hidden="true">
<div class="modal-content">
<div class="close-modal" data-dismiss="modal">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>
</div>
<div class="container-fluid">
<div class="row">
<div class="col-lg-8 col-lg-offset-2">
<div class="modal-body">
<div id="slider" class="flexslider">
<ul class="slides">
<li data-slide="3">
<h2>Slide 1</h2>
<img class="img-responsive" src="http://placehold.it/900x600/red" alt="">
</li>
<li>
<h2>Slide 2</h2>
<img class="img-responsive" src="http://placehold.it/900x600/red" alt="">
</li>
<li>
<h2>Slide 3</h2>
<img class="img-responsive img-centered" src="http://placehold.it/900x600/green" alt="">
</li>
<li>
<h2>Slide 4</h2>
<img class="img-responsive img-centered" src="http://placehold.it/900x600/pink" alt="">
</li>
<li>
<h2>Slide 5</h2>
<img class="img-responsive img-centered" src="http://placehold.it/900x600/pink" alt="">
</li>
<li>
<h2>Slide 6</h2>
<img class="img-responsive img-centered" src="http://placehold.it/900x600/pink" alt="">
</li>
</ul>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<script src="js/jquery.js"></script>
<script src="js/bootstrap.js"></script>
<script type="text/javascript" src="js/jquery.flexslider-min.js"></script>
<script type="text/javascript">
$(".portfolio-link").on("click", function(e){
$('#slider').flexslider({
animation: "fade",
directionNav: true,
startAt: $(this).data("slide-to")
});
});
</script>
</body>
</html>