From all the available reports the control rods were deployed to stop the reactions as part of the initial quake response. The challenge with nuclear fission is that stopping the splitting of Uranium does not immediately stop the production of heat. In very simple terms, as Uranium atoms split (fission) unstable isotopes are created that will slowly degrade to stable atoms. This degrading process generates heat and ionizing radiation. Normal shutdown procedure for a BWR like Fukushima takes about 10 days, most of which is monitoring the cooling system.

The damage to the fuel rods occurred after the primary reaction (Uranium Fission) was stopped. Since the reactor core is damaged it is possible that the reactor geometry has changed in a way to permit some of the Uranium to begin to fission again. Without thermal information from the cooling system (temperature rise vs coolant volume) this would be difficult to determine and is not very critical to the efforts currently underway. Reactor geometry is very carefully planned and it is at least equally if not more likely that the damage will actually make it harder to sustain Uranium Fission within the core.

The longer they can hold things together and keep the cooling water flowing, the better, for everyone.

-Eric