This problem apparently started after the battery was replaced. I eventually came to the conclusion that my Autodiagnos tester just wouldn't communicate with the gearbox ECU. There was no fault with it, just a comms issue with my diag machine.
I found the main CAN BUS connection point in main loom behind the glovebox. Out of frustration I ran in new sheilded twisted pair cable from the immobilser, instrument panel and heater control panel back to this point. I could then reliably talk to all ECUs appart from the gearbox. The only problem was that it still wouldn't start first thing in the morning. Checking cranking voltage, I discovered that the voltage would drop below 9 volts. I got rid of the cheap and chearfull battery, fitted a decent one, rechecked cranking voltage (now didn't drop below 10 volts) and then tested over a week. So far, so good! Well, I haven't heard from the customer yet!
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