My 50mm is the fastest lens I've got, so I tested with it. Friend of mine borrowed the lens for some shots using D700 and he didn't experience any focusing issues.
As I said - the problem that I experienced is not that the image is out of focus. It is that focusing before the adjustment and after with the same lens, same setup produced very different results - after the adjustment left sensors got better, right sensors stays almost the same and center (as I understand the sensor that is suppose to be the most precise) got much worse.
At this point I am going to wait for my camera to get back to me and then do more testing, as well as AF fine tuning to see where that will get me. I will update this thread with my findings after all those tests.