Hi there we've got the 1100 triple and have had the same problem a couple of times . As soon as we noticed we had it straight out of the water and gave it a good flushing through , revving it very high and i think it clears the carbs and anything else that seems to be hanging around in there.
I'm probably wrong.
Mind you its a long time since you started your thread and you've probably got a new ski now !!!!