[Eldarrion]

Main reasoning for that is because your jCarousel initialization isn't located in the $(document).ready, but is instead floating freely.

Finalized, the code should look like:

 $(document).ready(function(){
 	$("a#site").click(function(){
 		$("div.gallery").slideDown("slow");
 		$("span.menu").fadeIn("slow");
 		$("span.picture").slideDown("slow");
 		$("a#site").fadeOut("slow");
   });
	$("#pictures").jCarouselLite({
      btnNext: ".nextpic",
      btnPrev: ".prevpic",
      visible: 5,
      speed: 400,
      vertical: true,
	});
	$("#gallery").jCarouselLite({
      btnNext: ".nextgal",
      btnPrev: ".prevgal",
      visible: 5,
      speed: 400,
	});
 });

As for stuff hiding, the main cause for that is the following code:

$(document.body).click(function () {
      if ($("div:first").is(":hidden")) {
        $("div").slideDown("slow");
      } else {
        $("div").hide();
      }
    });

Where you're essentially telling it... "whenever I click on any part of the window, hide or show the first div." Also, I'd suggest you look into the #pictures gallery, because it doesn't seem to contain pictures, but htm files instead. Also... do have a look at the solution to your other problem in this forum as well, because I see you haven't implemented it either:

http://www.codingforums.com/showthread.php?t=158332