Pete Knowle again. I had forgotten I'd left this query open, so I thought I'd better update it.
I found the answer when I went back to take another look. I popped round the back to take another look at the flue and found to my astonishment that the owner had carefully taped a supermarket bag over it!!
Apparently after my first visit, when I left the multipoint without its outer casing, the owner had noticed a draft coming from the unit and decided to fit her own draughtproofing 'solution'. Unfortunately she forgot to tell me what she had done - resulting in half an hour's wasted time. Anyway, problem solved - the flame was simply suffocating in its own exhaust thanks to the bag on the flue - nothing very 'mysterious' at all.
Peter Knowle, November 2009