Distinguishing between the user scrolling and programmatically scrolling using Javascript

Use a variable to determine when you are scrolling programmatically

Example:

var programScrolling = false;

$('#element').on('scroll',function(e){
    if (programScrolling) {
        return;
    }

    $('#element').stop(true); // stop scrolling animation

    programScrolling = true;

    $('#element').animate({
        scrollTop:...
    });

    programScrolling = false;
});

Not sure if that is exactly what you want, but the concept should work.