If the EITMS is turned on the engine will have a little more shaking than normal, front cylinder is firing and keeping the engine going while stopped at a traffic light. I've had cage owners comment about my 02 FXD rockin' and rollin' when next to me at a light. The rubber isolators take most of the vibes out at speed.
It's as natural as huge **** and a sweet personality, actually they all shake at idle but smooth out with a few rpms. Nature of the touring bikes. I don't mind it at all.