Hm.
You have to specify window you clicked in Mouse.GetPosition(IInputElement relativeTo)
Following code works well for me
protected override void OnMouseDown(MouseButtonEventArgs e)
{
base.OnMouseDown(e);
Point p = e.GetPosition(this);
}
I suspect that you need to refer to the window not from it own class but from other point of the application. In this case Application.Current.MainWindow
will help you.