apply_filters() original:

function apply_filters($tag, $string) {
	global $wp_filter;
	if (isset($wp_filter['all'])) {
		foreach ($wp_filter['all'] as $priority => $functions) {
			if (isset($wp_filter[$tag][$priority]))
				$wp_filter[$tag][$priority] = array_merge($wp_filter['all'][$priority], $wp_filter[$tag][$priority]);
			else
				$wp_filter[$tag][$priority] = array_merge($wp_filter['all'][$priority], array());
			$wp_filter[$tag][$priority] = array_unique($wp_filter[$tag][$priority]);
		}

	}
	
	if (isset($wp_filter[$tag])) {
		ksort($wp_filter[$tag]);
		foreach ($wp_filter[$tag] as $priority => $functions) {
			foreach($functions as $function) {
					$string = $function($string);
			}
		}
	}
	return $string;
}

apply_filters() fixed:

function apply_filters($tag, $string) {
	global $wp_filter;
	if (isset($wp_filter['all'])) {
		foreach ($wp_filter['all'] as $priority => $functions) {
			if (isset($wp_filter[$tag][$priority]))
				$wp_filter[$tag][$priority] = array_merge($wp_filter['all'][$priority], $wp_filter[$tag][$priority]);
			else
				$wp_filter[$tag][$priority] = array_merge($wp_filter['all'][$priority], array());
			$wp_filter[$tag][$priority] = array_unique($wp_filter[$tag][$priority]);
		}

	}
	
	if (isset($wp_filter[$tag])) {
		ksort($wp_filter[$tag]);
		foreach ($wp_filter[$tag] as $priority => $functions) {
			if (!is_null($functions)) {
				foreach($functions as $function) {
					$string = $function($string);
				}
			}
		}
	}
	return $string;
}