I'm having the same experiences as the other posters and all I can add is that a system restart didn't help (not that I thought it likely). I started watching S5 a little over a week ago and am as certain as I can be that the "Ray Donovan / Episodes" menu showed a total of 60 episodes available, 12 for each season. However, it wasn't until I tried to watch E9 on 12/24, that I noticed it was not listed. I ended up watching it using the Showtime app on my Roku stick.
Same problem here. We called Xfinity and they submitted a ticket today. They said it takes 24 hours so hopefully it will show up tomorrow evening!