Just got off the phone with Nikon's tech support (whom I'm impressed with, service-wise). They couldn't tell me exactly what the issue was, but they suspect that there wasn't enough contrast in the single AF point to give the camera accurate focusing data at that long a focal length. The reason they couldn't tell for sure is because I wasn't able to give them a .nef RAW file straight out of the camera (I'd imported them to Lightroom and converted them to .dng which strips a lot of the diagnostic metadata, they said). Had I used Nikon Capture NX (Nikon's post-processing program) that they'd have had no difficulty determining the problem because all the metadata would have been there.
Might have to play with Nikon Capture for a bit, now.
Anything worth shooting is worth shooting twice. Bullets are cheap. Life is priceless.
For the focus issue, a few things might be going on. The first is that often times the AF sensor may actually be slightly larger or even slightly misplaced, as those markings are on the bottom of the pentaprism and the AF sensors are located at the bottom of the mirror box (under the sub mirror), so it is possible that even though the marking for that AF point was on your niece's face, the actual AF point might have been picking up the girl behind her. Also, I'm not sure if this is true or not with the D3 or not, but often times the periphery AF points aren't "cross type", which means that it may only find focus on a vertical area of contrast but not a horizontal one (or vice versa), and they tend to be not quite as accurate. You can sometimes tell if this is going on if the camera will find focus in landscape but not portrait (or again, vice versa). It is also possible (but not very likely because you would have noticed in other shots) that that lens or the body is out. You can test it by mounting the camera on a tripod, locking the mirror up and shooting a focus chart. That link is actually kind of nice because it has a fairly in depth discussion of how AF works.
As for Lightroom, you can have it keep you files as *.nef s if you want (or you should be able to, I have it working with my raws), and for all intents and purposes, it seems to work the same as if you convert to *.dng.
Great thread guys! (sorry for being last kid to come down to the dinner table). FlyBoeingJets, your industrial pics were intense! PM, D300, eh? Nice! I had lost mine to eBay... well, that is, sold it on eBay after hopping up to a D3 and realizing I don't really need 2 cams just yet. What lenses are you sportin'......?
Here's a couple my HDR's to add into our magic stew:
all pics are actually from just one raw file (eek! no bracketing!)... i'll post some more soon!
hopefully this thread isn't dead; if it is this it's time to wake it the **** up!