Ok, so after getting a second CableCard for the Tivo HD, I had the same issue: Local Channels but not cable channels. I could also get the music channels. Basically anything in "the clear."
So I had a Comcast tech come out on Sunday, and they still could not get the M-Card to work. So he decided to replace it with two S-Card's and we were able to get this working. However, as I was in a hurry to meet my wife for lunch, I did not take the time to check our Tivo upstairs. This was a mistake, as later in the day, I discovered that when the central office took off my second M-Card they also disabled my primary on. As a result, I now only have channels that are in the clear on my primary Tivo. (argh!)