>> Do you think having two NEF Codec's (Ardfry Imaging and Nikon's) would have any effect?
That is called "intentionally creating DLL havoc"
Think about it. A NEF codec is an interface between image files and various apps that are displaying files to you. It is all done behind the scenes- you don't pick which codec you want to use each time your app displays an image.
You need to make that choice in terms of which (ONE)codec you run. You should only have one installed.
I use iMatch, which is an image cataloging app that is heavily reliant on these WIC codecs. I have seen iMatch problem reports similar to yours, and then resolved by uninstalling BOTH codecs. You should reboot in between uninstalls, just to make sure they are cleanly uninstalled.
I've bounced between the Nikon and FastPictureViewer codecs, trying to optimize my iMatch performance and resolve a strange bug iMatch seems to have with FPV, but I always uninstalled and rebooted in between installs. Never had both live at once. I'm not familiar at all with the codec you use.
Although CaptureNX and ViewNX may both use Codecs, they use them differently. Capture probably only uses codecs to show you the film strip thumbnails. ViewNX is likely using the Codecs to display the full size embedded JPG image - unless you configure it to always render NEFS, in which case it would act more like CaptureNX (and performs more like it too in that mode!).
Thinking about it, Nikon's apps may not use the WIC codecs at all - as I recall they run fine without installing it (Nikon's). But you should only have one installed and since you are having problems this is a good problem solving procedure just to eliminate this possibility.
I suspect Process Explorer will not help you with any codec problems because that runs through the Microsoft WIC dll (WindowsCodecs.dll). Having never delved into the innards of the WIC codec structure I'm not sure what else might show up in Process Explorer to point out some sort of codec collision (especially from running 2 different versions at once, as you are doing now).