I'm a NPS member and professional photographer in NYC.
Prior to 2013, I had my equipment repaired locally at Phototech. The convenience of not having to deal with shipping was great and they work they did for me seemed fine. After comparing the cost of repairing a TC at Phototech vs. Nikon (Nikon was significantly cheaper—according to Phototech this is because Nikon doesn't have to pay for parts?), I decided to try using Nikon for awhile. Plus Phototech could not service my 70-200mm f2.8 VRII.
So in Feb. I sent a 70-200mm f2.8 VRII lens to Nikon a checkup and calibration. Mostly I wanted them to recalibrate the AF as I'd needed a -20 adjustment (on multiple bodies) to get good results and worried that this "solution" just added greater uncertainty as far as accurate autofocus goes at a variety of distances. I shoot action in dark environments so AF accuracy is critical. The lens was returned clean and supposedly adjusted (under warranty). Unfortunately the AF calibration had not changed—I still needed -20 Fine Tuning to get sharp results (on a second body an adjustment of -20 was not quite enough). I recently resubmitted the lens to Nikon for re-repair and am waiting for it to be returned.
In June, I sent a 24-70mm f2.8 lens for a checkup and calibration (it'd been acting up a little). Prior to submitting the lens, it generally needed a -3 to -6 AF Fine Tuning adjustment. When it was returned ($400 later--a part was replaced), it looked great, but testing showed that it needed -20 AF Fine Tuning. I am returning for re-repair.
Needless to say—2 of 2 lenses in 4 months returned to me with major calibration issues is a huge problem. I have NPS loaner equipment this time (thankfully), but the the hassle of this has been tremendous and I'm left seriously considering my options. (id)
Thom's comment: AF Fine Tuning issues are amongst the most difficult to get fixed reliably in one pass through NikonUSA, at least from the comments I get from readers. There's a tricky problem here: no specific "adjustment" point really exists for AF Fine Tune. Thus, gettig a lens tuned differently is sort of a trial and error type of procedure.