It seems that you have checked all the things that would be obvious, so my first thought was something not so obvious. I know next to nothing about this bike. But having said that, if it's like most, it has a separate exhaust pipe for each cylinder and you are measuring the temperatures there. Soooo - could it be that there is a thermal conduction difference between the colder pipe and the others? Maybe it's not tight against the cylinder port similar to the others? Or maybe it's more tight. Maybe the others have a mating gasket and this one doesn't. If the pipe has better thermal conductivity to the exhaust port on the head, it would probably run cooler, wouldn't you think?
Another thought, maybe there is more exhaust back pressure on that cylinder.