You know what I noticed:
I tried out my friends AP for the weekend back during Thanksgiving, and it was cold. When I did that the stutter was gone. I know that the ECU is effectively reset when putting a map on, so I figured that was why it was gone, and eventually it will come back.
The weekend comes to a close and I take the AP off, and go on my merry way. The thing is, its like a month and a half later, and I still don't have the stutter. I have driven at least another 1000 miles on the car, so it should have showed up.
Now here is my theory..I don't know if it holds water, but here goes.
I bought my car in July, and at the time, I didn't feel too much stutter..at least enough for me to complain about it. So I am driving it for like 3-4k miles and then Fall hits and things start to cool down. Then I start getting the stutter, so I am like..oh it is because of the cold weather that it is getting more apparent.
I then do that AP stuff mentioned earlier Thanksgiving weekend, effectively resetting my ECU. But when the ECU was reset, it was COLD outside, like 35-40 degrees, and the weather has been like that ever since then. Is it possible that the COLD brings on the stutter, and that by reflashing in the cold, and having the ECU relearn in the cold, it has learned to control or reduce the stutter?