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If the Pektron is immobilised (which I guess means if the LED is lit or flashing) then it will not allow a diagnostic session to start.

On a late Pektron like yours if you unimmobilised the car using the EKA then it will allow a diagnostic session but it won't allow you to code in a new fob; you can only code in a fob if you already have a fob and used it. It wouldn't surprise me if the later ones won't let you change the EKA with only the EKA either.

I will look into your specific problem but it will take a little work because I have to fit the later Pektron (I have one) to my Rover 25 or wire it up on the bench.

Whilst you are waiting there is a video of me entering the EKA here

It is quite tricky to do and I only get it right 50% of the time and I'm not sure why.

Also you should check in live data that the door switches are working properly.