I am seeing this in a game I am playing too. I sent a bunch of horse archers into Amurite lands to pillage and destroyed quite a few nodes. After peace was restored, the Amurites refused to rebuild the nodes and instead built mines/cottages/farms on top of the fire/air/law mana that was left behind. the only thing I can think of is regular mana is class rawmana while an improved(fire/air/law) mana is just class mana and the workers can not improve non-rawmana features???