Mine ran rough a few times just after starting it as well. It only did it when it was parked for the whole weekend or a week. It hasn't done it in a while, and when it did, it only did it for 10 to 20 seconds. I haven't tried to go anywhere while it was doing it so I don't know if there was a loss of power. I have no idea what would cause it... My guess would be fuel line or fuel pump. I've had problems with my fuel pump wire harness under my rear seat corroding... I rewired it and I havne't had the rough start since... but then again, it hasn't happened often enough to draw that conclusion anyway.