For microwave hot chocolate, why pour the hot milk into the chocolate rather than mixing the milk with chocolate then heating?
You were using real cocoa powder, not an instant drink. You probably cooked it in the microwave, or at least part of it. When milk over the powder, it was certainly not hot enough to cook the powder. So beyond any lumps that might have come together (you don't describe if you took measures against it), there is certainly a taste difference between cooked and uncooked cocoa.