Solved. The fix was replacing the ECU. Just swapped it out with a second hand one of eBay and end of problem. I suppose it might have been disconnecting the battery resetting something rather than the ECU.

Hi, my beloved 1998 P38 4.0 V8 automatic RR has developed a bizarre interimittent fault that I cannot find discussed elsewhere - I have spent days searching forums and asking garages. So just in case someone out there has any idea what could be behind it or even better knows the magic...