This response does not apply to the original post....I missed the "AT" in the title.
Manual transmission I assume, so the tune would not be affecting the shifting.
There is a TSP out on the manual transmission having difficulty in shifting. It's on this site. Search for it. It may even be on this page, or page two, as folks were posting on it yesterday.
It is better to keep your mouth closed and let people think you are a fool than to open it and remove all doubt.