I will say I think the shutdown when going into "full hybrid" mode may be a little more noticable than the quick warmed-up shutdown. I can't say if this is what's going on, but it's a possibility. Pay attention to whether the car is shutting down right away, or if it takes a good 7 seconds for it to shut down, when it does the "rough shut down". If it's only doing it after the car's warmed up and it takes a solid 7 seconds or so for the rough shutdown, it may be something different about how it does the shutdown when kicking over to "full hybrid".