I have the exact same problem. I have the latest server update. I tried resetting both HD Homeruns connected and rescanning to no avail. I cannot record anything from CBS since the program guide is not recognizing the CBS channel correctly.
I think I may have solved this. Delete your DVR and set it up again. The new setup asks for your zip code. Once you run the setup again it appears that CBS is now recognized correctly. I did put in a zip code that is more closer to the main metropolitan area instead of my own zip code. I am not sure if that made any difference.