Executive Summary: Yes, I believe my camera has an issue. No, it's not something that would prevent me from using the camera.
The setup: For this test, I used my newly acquired 50mm f/1.8 AF-S. I had done an earlier test just on the left side an 85mm f/1.8D. For those of you who read the Nikkor Lens forum, that 85mm was the same lens I used for a 45-degree angle test.
I placed my Lens Align Pro at the edge of a desk as show. I then placed a Nikon accessory box first to the right and then to the left of the Lens Align unit, ensuring the box was also to the edge of the desk. I then lit the rig with a single wide-spectrum, daylight balanced CFL in a white reflector:
I set up the camera on a tripod about 50" from the target and focused on the center of the target, and took reference shots with both Live View and standard focus using only the center focus sensor. I found that with this combination, the lens showed a typical amount of variance for an AF-S lens test, with results bracketing the zero mark. This is a typical result:
This image and those below was taken from a screen shot of View NX2 and resized in PS6. I did not sharpen or try to correct the images. This particular shot showed a small amount of front focus, but not enough to make me want to fiddle with AF fine tune. YMMV.
I then tested the "in-between" left and right focus points. Now the AF system was focusing on the box instead of the Lens Align target, but these showed similar results to the center sensor.
Next, I shifted to the extreme right focus point. These shots showed higher variance. Here's a representative shot that showed enough back focus to be a candidate for tweaking, but other shots were closer, with one being spot on.
Finally, I shifted to the extreme left focus point. I still saw variance, but now each shot showed some back focus. Here is a typical and "best" shot for the left focus point:
Obviously, my testing technique is far from perfect, and at some point I knocked my light and had to repoint it. But at least to my eye, the issue seems to be there with both the 50mm and 85mm lenses. But for real life use, I'm just not all that worried. I don't use a single AF sensor all that often, and quite honestly I'm not going to rely on a non-cross type sensor for critical work. Years of doing the focus in the center, recompose and shoot shuffle are a hard habit to break.
So do I believe the problem is real? Yes. Do I believe it's as big a deal as some of y'all? No. Once things get a little quieter, I'll probably send my camera into Nikon for a quick check, but in the meantime my plan is to relax, don't worry and keep shooting.
One of the biggest mistakes a photographer can make is to look at the real world and cling to the vain hope that next time his film will somehow bear a closer resemblance to it. - Galen Rowell