There is a video, somewhere, that tells the user to
select the corners in an X shape, but it should be a U shape: top-left,
bottom-left, bottom-right, top-right. Perhaps you're doing that, or maybe
you are selecting the very edges of the squares instead of the
centers.
HOWEVER, if you have CS3, with the release of ACR
4.5 and LR2.0 last week, you can use the new Adobe Labs DNG Profile Editor to
create a custom Camera Profile that you select in place of the ACR 4.4 that you
see in ACR and LR, now.
Using Adobe's DNG Profile Editor to create profiles
for my camera, I see the same reduced color-error as when using Tom's script and
it only takes a few seconds to run, as opposed to 10s of minutes for Tom's
script.
Don't worry that it's called a DNG-something.
That's merely because the profiles you create are documented in the DNG 1.2
specification. The profiles work the same as the Adobe-supplied profiles,
for both RAWs and DNGs.
Besides the Profile Editor, Adobe Labs also lets
you download a whole set of profiles for each camera. Not sure what your
Nikon has, but my Canon has profiles named: Camera Faithful, Camera
Neutral, Camera Landscape, Camera Portrait, Camera Standard.
There is a FAQ and a Tutorial about how to create
and use the profiles.