Finally got the car back up and running after about 3 months off the road. The convenience control module had melted, this is what controls the central locking, the garage took the whole dash out, I bought a brand new one from seat for £400 and they fitted it, and it melted again when auto lock kicked in. Garage washed their hands of it and said they were out of their depth, so I took it to Seat, Seat had never seen anything like this ever, they contacted the top techs and they couldn't fix it, they spent hour and hours on it and gave up. I bought a used CCM off ebay and a used passenger door loom as a last resort, replaced both, coded my keys and made sure auto lock was turned off, and I fixed it. The issue all along was the passenger door alignment, if the door isn't exactly lined up to the millimetre, the car doesn't know if it's locked or unlocked and so keeps trying over and over to lock itself when in traffic when auto lock would normally kick in. The units were melting as the relay was overheating from repeatedly locking and unlocking the passenger door.
Had to also get a new battery as the car was sat off the road for so long, but all good again now and can concentrate on getting other bits sorted.