FocusedElement is not being honoured

As per FocusManager documentation -

Logical focus pertains to the FocusManager.FocusedElement within a specific focus scope.

So, its not necessary that element with logical focus will have keyboard focus as well but vice versa is true i.e. element with keyboard focus will surely have a logical focus as well.

As stated in documentation FocusManager.FocusedElement guarantees logical focus and not keyboard focus. So what you can do is create an attach behaviour similar to FocusManager.FocusedElement which will set keyboard focus on an element.

You can refer to this for setting keyboard focus using attached behaviour - Setting keyboard focus in WPF.

Code from that article -

namespace Invoices.Client.Wpf.Behaviors
{
    using System.Windows;
    using System.Windows.Input;

    public static class KeyboardFocus
    {
        public static readonly DependencyProperty OnProperty;

        public static void SetOn(UIElement element, FrameworkElement value)
        {
            element.SetValue(OnProperty, value);
        }

        public static FrameworkElement GetOn(UIElement element)
        {
            return (FrameworkElement)element.GetValue(OnProperty);
        }

        static KeyboardFocus()
        {
            OnProperty = DependencyProperty.RegisterAttached("On", typeof(FrameworkElement), typeof(KeyboardFocus), new PropertyMetadata(OnSetCallback));
        }

        private static void OnSetCallback(DependencyObject dependencyObject, DependencyPropertyChangedEventArgs dependencyPropertyChangedEventArgs)
        {
            var frameworkElement = (FrameworkElement)dependencyObject;
            var target = GetOn(frameworkElement);

            if (target == null)
                return;

            frameworkElement.Loaded += (s, e) => Keyboard.Focus(target);
        }
    }
}

Use in XAML -

<UserControl xmlns:behaviors="clr-namespace:Invoices.Client.Wpf.Behaviors">
    <Grid behaviors:KeyboardFocus.On="{Binding ElementName=TextBoxToFocus}">
        <TextBox x:Name="TextBoxToFocus" />
    </Grid>
</UserControl>

FocusManager.FocusedElement="{Binding ElementName=Username}" sets logical focus but not physical focus.

Physical focus is the normal focus, logical focus is kinda a second focus which is still a little bit buggy in wpf 4.0.

I would suggest you to use Keyboard.Focus(this.Username).