I bet it's the same problem I had. I had Comcast come to the house and they discovered that my cablecards weren't set up properly back in the system. Specifically they said something about the rate they were set up was actually for a cablebox, not a cable card. We could verify the problem by entering the IP Service screen of my Tivo Series 3's Cablecard configuration menu. I forget which but either the upload or download field was listed as "waiting for ACK" which means that it wasn't speaking properly to the headend (since the headend wasn't giving it all of the correct commands). We had to pull the cablecards, verify the serial numbers and resetup the entire thing. I'm not sure when this cablecard snafu happened, but I suspect I'm not alone and this programming move has only recently exposed the problem.
After that I stopped getting "not authorized" messages for my problem channels (which on a Tivo is getting thrown into a cablecard setup screen). My problem now is that some of the newest channels that just got turned on still don't have content on them. It's not all or nothing though....so I get BBC America HD now but National Geo Wild isn't playing. All other channels in the 1000s that are being relocated from the 180-399 block are working fine.