I would ring the factory since they just did the flash and see what they say
Thanks, Dave. I did just that earlier this afternoon, was put through to one of the technicians who suggested I check the connections on the 3 relays in the fuse/electrics box under the bonnet - which I've now done and still no joy. They said they carry out and test the flash on another car, so it can't be the ECU/reflash that is to blame. They also said not to worry and that it'll get sorted somehow.
I'll get back onto them again in the morning... (I can't help remembering your comment about opening the box, seeing a load of wires and not wanting to get involved with removing the ECU yourself!)