Do you have an open-ended ticket from Liverpool Street? I take the Eurostar quite regularly and, in my experience, it's invariably anything from a few minutes to half an hour late getting into St Pancras. Forty minutes sounds like plenty of time to travel three stops, but it wouldn't surprise me at all if it wasn't. Even if the train gets in on time, it can take anything up to a quarter of an hour to actually get out of the terminal building. Then you have a fair old trek to get to the Circle / Metropolitan line platform through the maze of tunnels that is now Kings Cross / St Pancras. Then, of course, that whole length of track is undergoing extensive renovation work at the moment - you're not <shudders> travelling on a weekend, are you?
Not forgetting the ongoing Paris Nord extension...