Are you including MotionPlus animations when exporting from CC3?
There are two types of animations that can be exported. Motion files only include animation data for the body, but MotionPlus data includes facial expressions as well including eye placement.
By default, your CC character's eyes will be looking straight ahead and this should be maintained when exported. However, if you include an animation that changes the eye position, then this will be maintained when you export. If this is not what you want then you will be better just exporting the body animation only (.iMotion, rlMotion) and the eyes should remain in the default position.