What do you mean by “custom camera settings”? Do you mean you’ve changed the Camera Raw defaults for a particular camera and those aren’t being seen until you do a Reset? Or do you mean some sort of Nikon-settings that Adobe never looks at?
Also at what point in the workflow are you converting these files, just after copying them to your hard-disk and before touching them with any other Adobe software, or after they’ve been adjusted in Nikon software, or after they’ve been adjusted in Bridge/ACR, initially as NEFs?