I don't know of any known D700 problems. I use the following AIS lenses on my D700 with pretty good success, 24mm f/2.8, 28mm f/2, 35mm f/2, 50mm f/1.2, 70-150mm f/3.5. The faster lenses work out the best for on-screen focusing, the 28mm f/2 is my favorite. I also use the green-dot, but I do have to be very careful as the green-dot in-focus indicators can give some puzzling results. I struggled over the word "puzzling" in the previous sentence, the results are not "false" or "false-positive" or "incorrect" it's just the the dot-indicator can be difficult to get a "lock". I think that's a measure of just how much jiggle we add to the situation when moving the focus ring.
I've had batches of images where I would swear that they were in-focus at capture time, but later review show a consistent error. In all cases where I've taken the time to deconvolute the results, it's pretty clear that it's my error - typically picking the wrong or confusing (to the camera) focusing target.
I always use the center AF spot for manual focus. I also run my shutter speed up a bit because I find that I hold the camera more rigidly when I don't have to have one hand more or less free to turn the focus ring. If I'm using the screen over the green-dot, then I pick a clear area between the AF brackets to attain focus.
I can't close focus my 50mm f/1.2 at f/1.2 on real world targets without using Live-View.
Over the years, I've found many ways to do it wrong and it always seems to show up on targets where I really want the results. I wonder some times if adrenaline play a factor - causing me to hurry, shake, use faulty judgment, etc.
Maybe we could tell more from a sample image.
Roger It's still, ISO, aperture and shutter-speed, right?