I encounterd the problem while configuring joomlacomment. I entered the configuration menu and the hole page got messed up. It happened becuase of my CVS hidden folder.
At administrator/components/com_comment/library.comment.php I changed line 285
from
if ($file != "." && $file != ".." && is_dir("$path/$file") )to
if ($file != "." && $file != ".." && is_dir("$path/$file") && (strpos($file,".") > 0 || strpos($file,".") === false))