This was posted on another forum after my original post. Gives a great explanation:
That bulletin has been discussed previously. There are two switches that need to be closed in the ignition switch assembly.....one turns on the ECU, the other triggers the side stand/neutral clutch lockout circuit. If you turn the key too slowly the ECU turns on before the second switch is closed and the ECU sees a fault and you get a 'check engine' type light on the dash. Evidently the newer electronics turn on the ECU very quickly compared to older versions. Only way to clear it is to reprogram the ECU, that is what the bulletin does. It reprograms the logic so the ECU gives more time for the second switch to be closed. Yamaha dealers are very familiar with it.....they have a database which they log onto and it tells them if any outstanding bulletins or issues apply to any particular bike. Takes about 30 minutes.