TuneECU (v5.5.x) told me to turn off the ignition for 5 seconds and on again, just as the written instructions said it would. That is probably the start of your issues, what version TuneECU are you using?
When you started the engine, did you hold the start button until it fired, or like me did it crank for longer than normal so you let go of the button and pressed it again? I think that's what tripped my code and after the restart it cranks for longer to check everything and interrupting that was not good for it. My 2c...