Can AF Fine tuning be non consistent?
but rather the AF of the body/lens combo as a whole. Different lighting conditions are a bear for AF from what I've noticed.
My D7000 focuses like a champ in broad daylight or other very well lit areas, and it definitely becomes less reliable in low light. My way of alleviating this is by using an SB-900 indoors, but oddly enough the camera tends to backfocus with the SB-900's AF illuminator. Because of this, I've got -5 dialed in when I'm using the flash, and I turn it off otherwise.
I do get different results under different lighting, whether its fluorescent, tungsten, or whatever the case, so I try to use the flash whenever I can for at least some degree of consistency.