I have been using the D1x for about a year and have never seen this problem under any lighting conditions. But one thing is for sure: the Auto tone setting, Custom setting #24, is not your problem since this has no effect on the raw NEF files. If you have eliminated your lighting setup as the source of the problem then I have only two other guesses: 1) the NEF conversion program you are using or 2) an actual problem with the camera that needs fixed by the factory. Let us know how you solve this this one!
This photo taken with a D1x, RAW, converted by Bibble 2.99. Only minor color correction and dust spot removal in PS.
