I was up very late last night working on some stuff (and trying out various features of Channels DVR Beta, I must admit), and I noticed that my web guide was very wonky. Many channels for that timeframe (12 Midnight to around 5AM) had disappeared completely, even though they still showed in my TVOS guide. The ones that had disappeared completely seemed to be the ones that I had marked as HD in the web interface yesterday (legacy DUAL tuner user).
Other channels, all SD, had only sporadic data showing, if any–an hour of programming here or there.
The guide seemed to correct itself after around 5AM.
Is this related to the 5AM updates?