This is apparently a known issue of incompatibility between TWC and TiVo, which I have been trying to resolve for over a year. But there may be a solution that works, as I have recently discovered:
The cablecard people at TWC blame it on TiVo and vice versa. However, I finally got a lead from a TWC Cablecard person who gave me a case number that is over a year old: 120705-008204; no other tech at TWC has given me this case number, though they have told me that this is a known issue and tere is a fix, which never helped me. I contacted with TiVo chat about this and they said there is no patch or anything to push to the TiVo. I then called instead and talked to Tim who was much more helpful. He told me that what I could be experiencing is some residual mapping from before I moved, and that TWC's mapping might be causing the problem. After researching a bit, he said that I might be onto something with the case number. This was above his level, he said, but he said he had it on the desk of a (the?) head technician; this was last Friday, so he said it might take past the weekend to resolve, but he felt that the answer might come in the next few days, but wasn't sure if it was something that would be automatically updated on my machine or something I would have to apply myself.
One other thing I should definitely point out is that my problem was ONLY with certain seemingly random HD channels, and no SD channels. So I have just been watching SD on the few missing HD channels (in my case ESPN2, CBS, Disney, and a few others), unless I want to record something on them in HD, in which case I turn off the tuning adapter and I actually get those channels in HD but lose most of the others. I noticed only yesterday, when I recorded two versions of a program, one in HD and one in SD, that both took up the same amount of space on the TiVo's hard drive. So I looked at both recordings and they were actually both in HD (recorded one on ESPN and the other on ESPNHD). I looked at several channels and it appears that now, all channels I receive are HD unless they are not broadcast at all in HD. I am not exactly sure if this is the "fix" being applied, but it does seem strange giving the timing, because I noticed this exactly one day after my conversation with TiVo.
In any case, while those few HD channels I was not receiving still do not show up (I get a black screen and error message), I can just change the channel to the SD broadcast and I now have the programming in HD. Again, whether this is the "fix" or not I do not know, but you might want to give that case number to Tivo and see if you can make headway with it. I'd be interested to know if you experience the same thing. Sorry for the long reply.
Now if only TWC would set their CCI byte for cable to 0x00. But that won't ever happen. Good luck!!