Run the KOEO test again and when the codes are starting to register on the check engine light, unplug the jumper.
If the condition is not cleared the vehicle will still show the code next time the process is performed.
If your vehicle has a relearn procedure, you may need to do this. After removing the battery for more than 5 minutes the Keep Alive Memory is cleared, and the vehicle will not perform the same for a period of time as it 'relearns' after power is restored and the engine is turned back on.
What type of transmission do you have?