From Elon's description there it sounds like he believes the self-destruct system did immediately activate, but there wasn't enough detonation cord for the resu

From Elon's description there it sounds like he believes the self-destruct system did immediately activate, but there wasn't enough detonation cord for the resulting explosion to immediately destroy the spacecraft at that altitude. That's where the "40 seconds" number comes from. He also suggests that re-qualifying the abort (self-destruct) system is the item that will take the most amount of time before they'll be ready for the next launch.