One of the problems I ran into with the megasquirt was after making changes to the AFR tables while on a dyno and seeing gains from these changes...then after each dyno pull the bike would need to be turned off, then on, to be back to a good idling state and be able to make more changes or another pull. Have you ran into anything like this? This also happens when out racing...the bike would need to be shut off then on.
Have others ran into this problem?