What would be non-emissions related that would cause a check engine lamp? Thats what the lamp is there for right? Even if its a transmission problem the whole reason it turns on the CE lamp is because it effects emissions. My guess is either the scan tool they used was having issues or there is a problem in the car. Try a different scanner 1st and confirm that its not just an issue with the specific scantool. If no OBD2 scan tools will work then check that the cover to the 20-pin connector under the hood is installed... it needs to be present. Check fuses. Call your dealership and make sure that you have no open emission campaigns (recalls) If all else fails pay the dealer to diagnose why the vehicle will not communicate with the scan tool.
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