Have you tried calling Deactivate(false) on the window view-model and then call Activate()?
If I remember correctly, as long as the window view-model is not activated, the window is re-focused upon activation.
Edit: On a side note, depending on the Conductor/pseudo-Conductor you use to manage your screens, the IsActive property could be false even if a Window is still present. If a screen has IsActive = false, it doesn't mean necessary that the attached view has been closed. It just means that it is not the currently active element (in the context of its parent Conductor or presudo-Conductor).