Well I think I've figured it out.
You said that your contactor is switched by the microswitch on the throttle pedal. What will happen when you apply throttle with no power is the duty cycle will rise to increase current. Current wont increase though because there is no voltage coming into the controller. When you get to the point of the throttle that closes the contactor, you are at 100% duty which means only the mosfets are conducting. So, now the ugly. When that contactor closed, 100% of the battery was connected to the motor. this means huge current and it happend super fast. If the current sensor was working, it would have tried to limit current. Also, Paul and I think that the first time it happend the fets failed shorted. The second time the contactor closed and finished them off.
This all explanes the fets being blown and the rest ok. If it was running the old firmware, that doesnt check for current sensor for safety. The new firmware > 1yr old, would have disabled the controller before it could even do anything.
Another thing. If you could take out the contactor and take it apart and look at the contacts, you will most likely find some serious pitting on it. If there are pits there, my philosophy is true.
Sorry to be the bearer of bad news
-Adam