No, I've never had a problem with the transmission. The only roughness I ever notice is if I had my cruise set at say 50 miles per hour, but I had to slow down to 30
MPH. When I hit the resume button, the car starts accelerating, and when it gets to 50
MPH, the car jerks just a bit as the transmission upshifts to 5th gear and releases the throttle at the same time. 50
MPH seems to be a touchy speed when it comes to the cruise control. I try not to set/use the cruise control at any of the shift points to avoid this.
I doubt you'd have any problem with it, but have you checked your transmission fluid level?