I still don't see any reason for the left column to have the gap at the top, but you do have a major HTML error in view source:
Code:
<base href="http://baratowatches.com/" />
<link rel="canonical" href="http://baratowatches.com/" />
<link rel="stylesheet" type="text/css" href="includes/templates/CUSTOM/css/stylesheet.css" />
<link rel="stylesheet" type="text/css" href="includes/templates/CUSTOM/css/stylesheet_css_buttons.css" />
<link rel="stylesheet" type="text/css" media="print" href="includes/templates/CUSTOM/css/print_stylesheet.css" />
</head>
<body id="indexHomeBody">
<div id="mainWrapper">
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Barato Trading Corp. - Watch Wholesaler</title>
<link href="/oxo-ecommerce/Template css-xhtml/css/style.css" rel="stylesheet" type="text/css" />
<link href="/oxo-ecommerce/Template css-xhtml/css/slideshow.css" rel="stylesheet" type="text/css" />
<script type="text/javascript" src="/oxo-ecommerce/Template css-xhtml/js/jquery-1.3.2.js"></script>
<script type="text/javascript" src="/oxo-ecommerce/Template css-xhtml/js/jquery.cycle.js"></script>
<script type="text/javascript" src="/oxo-ecommerce/Template css-xhtml/js/jquery.functions.js"></script>
<script src="/oxo-ecommerce/Template css-xhtml/js/cufon-yui.js" type="text/javascript"></script>
<script src="/oxo-ecommerce/Template css-xhtml/js/Comfortaa_400.font.js" type="text/javascript"></script>
<script type="text/javascript">
Cufon.replace('h1', { fontFamily: 'Comfortaa' });
Cufon.replace('h2', { fontFamily: 'Comfortaa' });
Cufon.replace('h3', { fontFamily: 'Comfortaa' });
Cufon.replace('h4', { fontFamily: 'Comfortaa' });
</script>
<script type="text/javascript" src="assets/js/font-delicious.js"></script>
<!--[if gte IE 9]>
<script type="text/javascript">
Cufon.set('engine', 'canvas');
</script>
<![endif]-->
</head>
<body>
<div id="Layout">
<!-- BEGIN HEADER -->
<div id="Top">
<div id="Logo">
You have inserted a second HTML document inside the original Zen Cart page, and that may be messing something up.