Cheers for the responses, I have a fender extender and today, whilst it was damp, I've ridden through torrential rain and never had an issue
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I'm thinking it can only be one of 3 things, 1 - maybe some ACF-50 got somewhere it shouldn't and caused a temporary problem (I did put loads on everything except brakes etc yesterday and idled the bike until most of it had burnt off the exhaust etc), 2 - the bike 'missed' after being ridden for a 30 mins at low/gear speed and by conicedence I had clutch in whilst changing gear and bike happened to stall mid-gear change (seems v. unlikely), 3 - there's a problem with the bike.
As I said earlier, I've had the bike 'miss a beat' quite a few times before, but normally when I've been going quick (5th gear on m-way) for about 40mins and then slowed down when I've got into the city centre....I mentioned it at the 4,000 mile service and the dealer said that this happens with the fuelling as the ecu changes to suit the riding conditions (is this true/possible?).
Cheers for the info about the ecu Baph, but as I usually ride the bike to/from work and the dealer is miles in the opposite direction, going there before having to turn the ignition off isn't really an option.