AJAX Chat Box Scrolling Up Issue

Hi I am writing a chat website and I have a problem with the div containing the messages. In the CSS the div containing the messages has overflow: auto; to allow scroll bars. Now the problem is when ajax is fetching the messages through a PHP script that fetches the messages from the database, you cannot scroll up. The AJAX refreshMessages() function is set to update every second using window.setInterval(refreshMessages(), 1000);. This is what I want but when I scroll up to see previous messages, the scroll bar hits straight back down to the end of the chat due to the AJAX fetch function.

Any ideas of what the issue is?

AJAX Code:

//Fetch All Messages

var refreshMessages = function() {
 $.ajax({
   url: 'includes/messages.inc.php',
   type: 'GET',
   dataType: 'html'
 })

 .done(function( data ) {
    $('#messages').html( data );
    $('#messages').stop().animate({
       scrollTop: $("#messages")[0].scrollHeight
    }, 800);
 })

 .fail(function() {
    $('#messages').prepend('Error retrieving new messages..');
 });
}

EDIT:

I'm using this code but it isn't quite working, it pauses the function but then the function doesn't restart when the scroll bar goes back to the bottom. Help?

//Check If Last Message Is In Focus

var restarted = 0;

var checkFocus = function() {
  var container = $('.messages');
  var height = container.height();
  var scrollHeight = container[0].scrollHeight;
  var st = container.scrollTop();
  var sum = scrollHeight - height - 32;
  if(st >= sum) {
     console.log('focused'); //Testing Purposes
     if(restarted = 0) {
        window.setTimeout(refreshMessages(), 2000);
        restarted = 1;
     }
  } else {
    window.clearInterval(refreshMessages());
    restarted = 0;
  }
}