Is there such a feature built into the ECU? I have never heard of that. Not saying you're wrong, that is just news to me(TIMMYDUCK @ Oct. 28 2006,19:51) Here is my wild guess.
With the Power Commander installed.
You are exceding the horse power restriction built into the ECU for first and second gears.
(Silly safety concerns.)
As such when you reached that Hp threshold in second the ECU sent a signal to cut power.
Don