I am using Simple:Press in Wordpress, and that i come with an Ajax auto-refresh code within the header, which refreshes Just the div which has the latest thread posts. The page refreshes all right, but will not load in almost any new posts for the reason that thread.

Here's the code during my header:

    <script>
    var refreshId = setInterval(function()
    {
        $('.sfposttable').fadeOut("fast").load('response.php').fadeIn("fast");
    }, 60000);
    </script>

Any ideas why the div refreshes, but does not pull in almost any new posts?

I believe make use of first

$(document).ready(function() {
    var refreshId = setInterval(function()
    {
        $('.sfposttable').fadeOut("fast").load('response.php').fadeIn("fast");
    }, 60000);

});

This is a working example: http://jsfiddle.net/943UA/

Also you might want to alter the refresh time: 60000 -> one minute allow it to be 2000 -> 2 sec for test purpose.