Single point AF-C: good, that's the easiest to control.
AF target: You should load the original out-of-camera file into ViewNX2 and see which AF target was locked on. Often when these things come up, folks are quite surprised. Sometimes I find that a very well focused image had no locked on target, but often I find that one that is soft or just out of focus was either not locked on at all or that a different target was used than was expected. I don't personally have this latter problem very often as I tend not to use the multi-point modes very often, but many other folks do.
You can also verify which AF mode you were using - NX2 does interpret all that metadata, which the Adobe products typically do not.
_____ Brian... a bicoastal Nikonian and Team Member
My gallery is online. Comments and critique welcomed any time!