You'll get your misfire code to pop up in the event that a plug either fails to fire or fires at the wrong time. Sometimes this is just a random occurence in engines - especially when being driven hard.

The fact that the dealer has a TSB on the incident and knew to flash the ECU means that there is a documented problem somewhere. It is likely that there was a batch of ECU's produced that had a less than optimal tune programmed into them. However, because this is a TSB and not a recall, most people won't hear a word about it unless they complain.

With your previous tune (and misfire) your car was probably defaulting back to a safer map where more fuel is dumped into the engine. This slows and cools the combustion process and helps to prevent damage. With your reflashed ECU you are probably running a leaner mix with better timing - this would account for your increase in performance.

Keep an eye on the car for a little while to make sure that your trouble light doesn't come back on. I wouldn't worry too much, though. Sometimes these things happen and it's unlikely that there's anything wrong with your car.