You must go back to immobilizer function and select pcm replacement follow promts
and it will program the keys, when done go to pcm and select also pcm replacement.
This will clear all the stored data from previous vehicle.  when you say new pcm do you mean new from the dealer or is new to the car.

 My friend you are replying to your post after good 7 months................!!!

So, at least you should have posted the out come of this vehicle............Did you be able to sort this problem as the other members advice...............?

Bit of your feed back would help many of use.............to prove that the tool is doing its job.............Or not........