I'd say it's still possible your issue is unrelated to the tune. I have Penner's tune installed in my GT and a few weeks ago my quick shifter spontaneously stopped working. A short time after that I got a message on the screen saying there was a transmission fault. De-selecting the shift assist in the menu made the transmission fault error go away. Took it to the dealership and they walked through the quick shifter troubleshooting steps and they found a pinched wire. They replaced the quick shifter and I'm back to quick shifter WITH the extra "oomph".
If you download the service manual (available in a few posts on here) you can walk through the troubleshooting steps yourself if you're handy. Involves pulling various connectors and running continuities.