Adding an animator controller rotates my character?

I rigged a model in Blender for animation with Mecanim. I've applied the humanoid rig setting and configured the character. When I place the character looking one way in the Scene view and push play, he is still facing the same way in the Game view. Now, let's say I add an animator controller. This time, when I push play he is facing the opposite direction and his body is halfway through the floor. Next, suppose I add an animation to that animator controller. Now, he's not through the floor, but he's still facing the opposite way, and he's running the animation correctly. Why does adding the animator controller rotate the character? To fix this, should I be playing with the original blender file? Or with the Mecanim configuration for the model?