This is a known but not well published problem with all tivos. It seems that all tivos use the time codes of the current brodcast channel being recieved to start the recording. The problem being that different channels are not necessarly in sync, time wise, with each other.

I believe I read this in one of the Tivo community forums.

edit: I've been reading the forums, lots of comments similar "late starts up to 3min". No real info. Supposed solutions include clear and reset, replace the drives, update to the latest (assumes your tivo is not been updated to the latest sftwr). Basically there is some problem that tivo hasn't/won't own up to, even if they do eventually fix it.

I haven't seen any late starts. More like early starts. For instance Stargate,Stargate Atlantis,BattlestarG. All these recordings started and ended a little early.