Bah, blasted IHD -> Plating -> Cooling Cell combo ... The IHD endlessly pumps heat into the plating because it can't see the status of the cooling cell, thus it melts during the cooling phase.
I have tried to make the reactor preempt this event and stop the generation phase earily, but I guess it wasn't enough. For now, it'll warn you of a melted component during cooldown and you'll have to manually scale down the genration time (to about 79% in this design's case) to get an effective EU/t rating.