About Alias seasons 4 and 5, I think it's exaggerated to say Jen's acting has not been up to par because of her personal life. All actors have personal lives which matter to them, and that doesn't lessen their talents.
I have not seen season 5, since it has not been on TV in my country, I have to wait for the DVD release; but I have watched season 4 and I think Jen was excellent in "Nocturne', she was up to her best in that episode.