I thought turning off the two transponder devices (sorry I forgot the specifics) was deemed impossible without manual action.
Bad electrical fire in the cockpit, lots of smoke, crew frantically trying to isolate source of fire, pulling as many circuit breakers and busses as they can, they pull those associated with the transponders (or the fire short circuits them). Smoke hoods have a limited life and eventually the CO gets them. Most of the pulled breakers remain in that state.
The Malaysian captain had a lot of hours and from everything I have read was regarded as a highly competent pilot. In some accidents the confidence that comes from that experience leads to mistakes in judgment-"we can work through this problem" rather than declare an inflight emergency quickly. A good example of pilot overconfidence with disastrous results is AA flight 1420 into Little Rock.