Yes. BUT for me it has always been an easy fix if Itake it to the right place. When I did my H/C/I, the car would NOT run right. I took it to a dyno shop that was reputable, they figured it out and fixed it and over and done with. I did not have the time to fool with that TWEECER when using it for MAJOR changes. I let the experts do it, I don't plan on making anymore changes now and it runs top notch and I KNOW the tune is totally safe. End of story. No more worries.
If you haven't, just take your car to a good tune shop or get a new trans, let them fix it and move on. If the problem is just the trans then get a new one.