*Update* hopefully now resolved
I had to go away for a week and managed to manually lock the car before leaving. However, whilst away a neighbour contacted me to say the alarm was going off, although it wasn’t constant nor too loud, so no need to rush back.
I got back today and intended to run the car round to a local garage, but the battery was completely flat, totally drained.
I managed to jump start it (easier said that done with a 5.2 v10) and thought I’d just try the reprogramming sequence again (one key in the ignition, the other in the door). But the car lights didn’t flash nor the alarm set as it was meant to, so I figured it still wasn’t working.
I then removed all the keys and thought I’d just press the main key buttons again and hey presto, it all worked. The alarm set and the doors all locked and unlocked as they should. I decided not to even try the second key though, as that was where all my troubles started.
So, should you be in a similar situation and the key reprogramming method doesn’t work, try disconnecting the car battery, as I assume that resets everything.
My battery is now on charge which I expect will take a good 24 hours and I’m keeping everything crossed that the problem doesn’t return.