It was my belief, and I BELIEVE that I had the experience, that using the kill switch COULD in certain extremes of temperature or whatever, fool the ICU into not knowing where it left off, then the idle is screwed when you restart the bike. My old Bonnie, always the kill switch on the Right Bar, 'cause the key is tucked away on the left of the headlight. On my speed triple I had this problem more than once, and at least twice on the ROCKET.
My belief is that if you have just done something abrupt with the throttle, revved it for example, and let it snap shut, the TPS is holding it open a crack to prevent the engine dying until it settles down. If you kill it at the same time, the power is cut with the TPS slightly open. Then when you start up, it thinks that is zero. If it is all screwed up, all you have to do is shut it off with the key, open the throttle and let it snap shut, then restart the motor. All is happy again.
That DOES NOT mean it is true, but it is what I heard, it seemed to be true, and so I quit using the kill switch. Maybe I was rolling on some throttle also, that will definitely screw the idle when you are starting. I don't use the kill switch and I try to keep from opening the throttle when I fire it up. Seems to work OK.