I solved it.
If someone else is having this same problem this is a 2.5.1 problem. I tried the same template with 2.6.2 and it works fine. The “exclude_category”-tag doesn’t exist in bookmark-template.php of 2.5.1 but it exists in 2.6.2’s bookmark-template.php.
2.5.1:
$defaults = array(
'orderby' => 'name', 'order' => 'ASC',
'limit' => -1, 'category' => '',
'category_name' => '', 'hide_invisible' => 1,
'show_updated' => 0, 'echo' => 1,
'categorize' => 1, 'title_li' => __('Bookmarks'),
'title_before' => '<h2>', 'title_after' => '</h2>',
'category_orderby' => 'name', 'category_order' => 'ASC',
'class' => 'linkcat', 'category_before' => '<li id="%id" class="%class">',
'category_after' => '</li>'
2.6.2:
$defaults = array(
'orderby' => 'name', 'order' => 'ASC',
'limit' => -1, 'category' => '', 'exclude_category' => '',
'category_name' => '', 'hide_invisible' => 1,
'show_updated' => 0, 'echo' => 1,
'categorize' => 1, 'title_li' => __('Bookmarks'),
'title_before' => '<h2>', 'title_after' => '</h2>',
'category_orderby' => 'name', 'category_order' => 'ASC',
'class' => 'linkcat', 'category_before' => '<li id="%id" class="%class">',
'category_after' => '</li>'