Well I have 8000 miles on my 12 Eco now and it has been the best vehicle I have ever owned but it has always shifted rough, Mainly into 3rd gear but you could always feel it downshifting when rolling up to a stop sign also, I just assumed it was the way it was suppose to be. This morning I was driving it and noticed it was shifting very nice and smooth, no downshift braking or the other little issues, I also noticed the the select shift was turned off (the numbers on the dash 1-6) if you push the + button on the shifter you can turn them off, I have had it turned on since I bought the truck because I kind of liked the display but anyway with the select shift turned off the transmission shifts very nice, I turned it back on and the rough shifting returned, Try it on yours to see if it changes.
If I understand you correctly (correct me if not), then what you are turning on/off is only the gear (1-6) display. I have mine turned on/off many times and have not noticed a difference in shift behavior. But then, I do not have a rough shift problem, at least not 99% of the time.
Yes, turning off the display also turns off the "Select Shift" program, that is the ability to limit how many of the 6 speeds are used, Mine shifts like it is in the "Tow-Haul" mode all the time but with the select shift off, it shifted very nice, maybe coincidence, I will try it this way for awhile to see.