Allora, ho fatto un po di prove ed ho modificato così
codice:
$(document).ready(function ()
{
    //Hide (Collapse) the toggle containers on load
    $("#workExtend").hide();

	$(".thumbContainer>a").click(function ()
	{
		$("#workExtend").show("slow");
		//$("#workContainer>div").filter(this.hash).slideToggle("slow");
		/*if($(this).attr("id") == 'thumbSkybox') $('#workSkybox').hide();
		if($(this).attr("id") == 'thumbExample') $('#workWebsite').hide();*/
		$("#workContainer>div").filter(this.hash).slideToggle("slow");
		return false;
	});
	$("#close-project a").click(function()
	{
		$("#workExtend").hide("slow");
	});
});
codice:
		<div id="workExtend">
            <div id="workHeader">
                <p id="close-project">
					Close Project</p>
            </div>
            <div id="workContainer">
                <div id="workSkybox" class="workDisplay" style="color : white;">
                    Work Skybox
                </div>
                <div id="workWebsite" class="workDisplay" style="color : white;">
                    Work Website
                </div>
            </div>
        </div>
		
        <div id="gallery">
            <div id="thumbSkybox" class="thumbBox">
				<div id="thumb_01" class="thumbContainer">
					<a href="#workSkybox" title="">
                        [img]thumbs/skybox/skybox-01.jpg[/img]</a>
					<div class="thumbOverlay"></div>
					<div class="thumbCaption">
						<p class="thumbCategory">Category</p>
						<h3>Amazing Image Title</h3>
						<p class="thumbText">
						   Lorem ipsum dolor sit amet, consectetur adipisicing elit,
							sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
						</p>
					</div>
				</div>
			</div>
			<div id="thumbExample" class="thumbBox">
				<div id="thumb_02" class="thumbContainer">
                    <a href="#workWebsite" title="">
                        [img]thumbs/webdesign/portfolio-01.jpg[/img]</a>
					<div class="thumbOverlay"></div>
					<div class="thumbCaption">
						<p class="thumbCategory">Category</p>
						<h3>Amazing Image Title</h3>
						<p class="thumbText">
						   Lorem ipsum dolor sit amet, consectetur adipisicing elit,
							sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.
						</p>
					</div>
				</div>
			</div>
			<div class="clear"></div>
        </div>
però la prima volta apre il link contrario a quello cliccato...