This is the left image of the pair. I remember vividly focusing on the large stone in the center of the foreground (confirmed when looking at the parallax in the foreground picture below). Not the greatest focusing point but the camera didn't complain when taking the picture so I can only assume it was good enough.
This is a close-up of the foreground in StereoPhoto Maker (I am using the stereo adjustment view at normal size). You can clearly see that the right picture is focused (expected, because that's where I actually focused the shot) while the left picture is blurry (not good).
This is a close-up of the background. Now, the right picture is blurry (expected) while the left picture is more in focus.
I've chosen this picture because there's quite a bit of distance between the foreground and background and it really shows where the left lens is focusing (it's focusing on something much farther than the right lens). With other pictures, when there's not much distance in the shot between foreground and background, it kinda seems that the left lens is blurry all over (probably because it's focused on a point who knows where).
This seems kinda strange that the two lenses are not focusing on the same point but, for the sake of discussion, let's assume that the two lenses do indeed focus independently. Then, this whole thing could very well be an auto-focus problem when the object that's focused on is not super well defined against the background, especially in low light condition just like in the picture above (I've seen the same thing happen in bright light though). I have no problem with the auto-focus not being able to lock but then, why does the camera say it can focus (focus light is green and camera beeps) and, more importantly, why is the difference in focus distances between the two lenses so large? And this leads to another question: If the two lenses focus on possibly two different things, how can the camera's software figure out the parallax in auto mode? The problem is that you have no idea you're out of focus until you go into StereoPhoto Maker and check the parallax at normal size. If the camera can't focus, no problem, just let me know about it and I can take the appropriate action (hopefully).
This is the wiggle (Piku-Piku) version from Start 3D (kinda like what StereoTracer from triaxes.com does). Obviously, if you only intend to show wiggles from your Fuji W3 mpo files, then being slightly out of focus on one lens may be the least of your worries.
Well, since then, I have taken a few more pictures in better light conditions and using better focus points, and it seems that the auto-focus behaves better. The two images are usually equally blurry under 100% magnification. Conclusion: the lenses on the Fuji w3 are not very good, to put it nicely.