The bold is here:

#navMainWrapper, #navSuppWrapper, #navCatTabsWrapper {
margin: 0em;
background-color: #abbbd3;
background-image: url(../images/tile_back.gif);
padding: 0.5em 0.2em;
font-weight: bold;
color: #ffffff;
height: 1%;
}

You could probably set #navCatTabsWrapper to a specific width to match the links on your main page. Increasing the padding-bottom should fix the part that's cut off.

Find this line in tpl_modules_categories_tabs.php and add the red part:
<li><?php echo $links_list[$i];?> &nbsp;|&nbsp; </li>