Did you go thru every station and thumbs up and down all the shows on the stations you watch? If you did this it could be working hard on getting you suggestions or it could even be recording HDTV and that is causing other things to slow down.

Since I just had this (F###ing power company) happen. Do you have your DirectTiVo on a UPS? My UPS didn't outlast the power outage tonight and when the power came back on the TiVo started recording shows from the middle. It doesn't say anywhere in the history of why it didn't start on time.