I have the same problem in the LA area. My system switched over from Comcast to TWC in October. Many channels are incorrect on Zap2It. I emailed them at the email listed on their website, and I'm still waiting. I have to manually record anything I want on those channels, since Replay isn't showing them. It's frustrating that Zap2It is taking so long.
BTW, I did select the TWC Rebuild listings, and the majority are correct, but any new channels have not been added. Also, several of the channels are showing Eastern times rather than Pacific programming.
In the past, Zap has been only a day or two behind the changes, it's been more than two months and several emails later and no corrections.