it sounds like even though its a fresh install of WP 3.1.2 that you are also using an existing theme that is using a deprecated function (you havent said so but im presuming),
if so paste this into your themes functions.php file (if your theme doesnt have one just create one and save it in your themes root folder)..
if(function_exists('add_theme_support')) {
add_theme_support('automatic-feed-links');
}