I think this behaviour was present in previous versions. It is not that DontDestroyOnLoad is cloning the gameObject, it is that the non-destroyable-object is persisting (as it should), but re-loading the level is also loading a new copy of the object (because it exists in the scene file).

If you want to reload the scene which contains the "Don't Destroy" object, but you don't want two copies of that object, you need to add some code which makes the 2nd new copy of the object destroy itself, leaving the first to persist. For example, a static boolean variable could be used to do this:

private var _sofar : float;
private static created = false;

function Awake() {
    if (!created) {
        // this is the first instance - make it persist
        DontDestroyOnLoad(this.gameObject);
        created = true;
    } else {
        // this must be a duplicate from a scene reload - DESTROY!
        Destroy(this.gameObject);
    } 
}

function Update() {
    _sofar += Time.deltaTime;
    if (_sofar > 3) {
        print("reloading level ...");
        Application.LoadLevel("test");
    }
}

That's normal, including versions before 3.1

An alternate approach to Ben's answer is to not create this persistent "state" object in your hierarchy at all, and have every scene check if the object exists, and create it dynamically (i.e. using some "LoadState" script), only if it doesn't already exist. This way, you always have just one copy of this object, and it doesn't matter what scene you start in.