I have this same issue with Rangers & Landers (haven't tried the Viper). The only pattern I've been able to sort of discern is that the problem usually appears if I launch them on top of a rocket stack, and usually doesn't if they are started & flown off the ground individually from KSC. When the reactor is started, it doesn't build any heat and will just sit at 100deg or less, saying 'zero efficiency' and not producing any power, making the craft unusable.