Righto, I found the bug. Except, it was my own stupid fault :o:
I had forgotten to copy over the new patch_ files from the utils directory into the main server directory, though I'd remembered to do opcodes.conf.
Nothing to do with the SQL engine or the database contents itself. I also spent quite a while going through diffs of the source files to the emulator, which made me realise again that opcodes had changed, but also showed me quite how much work KLS has been putting into the AA code - amazing!
Anyway I hope this helps someone else fix their server too if they have been as slack as me
Paul.