The Fuji W3 always seems to have one lenses slightly higher than the other. I have two of them and they both do this. I either manually align them or auto align in an app to do them in batch.
The Fuji W3 can't do close-ups very well due to the 75mm interaxial distance. It's great for anything more than about 1.8 metres away. For close-ups you really need either two cameras or a 3D camera with a much smaller distance between the lens. Something like the LG 3D Max phone (25mm) or the Sony TD30 camera (also 25mm, I think).