My 06 Grand Prix won't respond to my key fob.

I was using my key fob one morning to remote start my car it only responded
to the first lock and then it wouldn't start with the remote. Then I went outside
to check if there was any codes thrown and there was none. So I replaced
the battery still didn't work. I then took it into a GM dealership and they
tested the remote itself to eliminate the remote, so the remote is in perfect
working order. The next thing they did was program the remote the machine
they had hooked up to the OBD-II said it was programmed and low and
behold the darn thing still didn't work. The mechanic tried to program it a
second time but had the same result. So he said i could bring it in so they
could check into it further, he said they would look into the PCM next. So i
have two PCM's for my car one performance and the other is just the stock
that came with the car. Just replaced it and that isnt the problem either. And
the remote always worked with both PCM's. What's next? Is there some kind
of ECU programming?