Tornado chips can be very sensitive I have had one installed in my 94 +8 for over 14 years and the Check Engine light always comes on and showing fault code 48. I also have a non chipped 14CUX ECU which when installed does not activate the Check Engine light and shows no fault codes. The engine has run perfectly with the Check Engine light on, for rallies I remove the bulb as there are enough gauges to tell me if there is an engine issue. I would start by doing a complete reboot of the ECU i.e. disconnecting power to it for 30 minutes and then see if the issues reoccurs.

Bruce
1964 4/4 Series V Comp (Megan)
1994 +8 (Maurice)
2013 M3W (Olga)