I have had a similar problem with my car.
It is either one of 2 things.
If the car drives along fine and then jerks along suddenly and refuses to rev over 2000~rpm, your air flow meter (AFM) is playing up. Its probably best to find someone with the same AFM and test it in your car
If the car has a misfire depending on load/rpm, it is your coilpacks breaking down, replace them with splitfires and you will never have that issue again.
From my experience there is no difference between auto/manual ecu, The A/T light on your dash will be flashing because the shift ECU is not receiving a signal. Just remove the cluster and pull the light out if it annoys you.