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Thanks to everyone who responded to my question about the length of time
a gluten reaction lasts, and about the gluten content of quinoa and
amaranth.  The general consensus was that from one accidental exposure,
a reaction could last a few hours to a few days, therefore my son's
reaction last month and this month to the cookies I made him would be
consistent with a gluten reaction, especially since he ate the offending
foods more than once before we figured out what was bothering him -
though I didn't believe at the time, nor do I now have any evidence,
that they contained gluten.

I still am not sure what to think about the quinoa/amaranth controversy.
As I stated in my post, I was aware that the CSA prohibited them.  I was
also aware that every other celiac on the planet, including the CDF and
the proponents of the GFCF diet for the treatment of autism claimed they
were gluten free, though it was possible for a celiac to have an
additional intolerance to those grains as well. Just as a celiac can
also be dairy intolerant, that intolerance is not part of the celiac
syndrome, nor does cow's milk contain gluten.  However, I did hear from
one individual who admonished me for feeding my child a "low-gluten
grain" such as quinoa or amaranth, and warned me to be a better mother
by being more strict with his diet.  This was a difficult thing for a
mother to read, especially since he has been gluten free for more than
14 months, and this is the first bad reaction he has had to anything I
have fed him in this amount of time.  And I didn't feed him gluten, to
my knowledge, certainly not on purpose!  Am I wrong on this?  Many of
you confirmed that these grains do not contain gluten - haven't there
been scientists who have looked at them to determine their chemical
composition?  What do they say?  For us, it doesn't matter, as my son
obviously has a reaction to them, and so whatever the reason for his
reaction, be it gluten or a plain old allergy to them, he won't be
having any more of them!  I have heard the same argument made for teff
and buckwheat, by the CSA, but understand that most celiacs have no
problem with them (especially since buckwheat is a berry, not a grain in
the first place).  I guess to be on the safe side, we will steer clear
of those since it is obvious he is one of the more sensitive celiacs.

 I heard from many listers who had additional intolerances - to soy,
corn, rice, kamut.  One person could eat NO grains of any kind, and had
a classic gluten reaction to them all.  A few people pointed out that we
might be too quick to blame his diarrhea on the foods, when it might
just be a flu bug he got.  I suppose that is true.  As I learned even
adult celiacs who have been doing this awhile sometimes don't know if a
sour stomach is gluten related or not.  And someone else mentioned that
his system might not be ready for the new foods right now.  One person
thought I meant black stools when I mentioned the dark diarrhea he had,
and suggested having him tested for parasites, but I only emphasized
that fact that it was dark because his "normal" poop is so light
colored, which I understood to be a sign of nutrient malabsorption, and
yet when he has diarrhea it is dark, which is supposed to be
preferable.  Don't know what to think there.

 We tried Seren-Aid (Klaire Labs) last month to quell the reaction, and
are trying Enzyme-Aid (Kirkman Labs)this month to try to curb the
diarrhea.  So far, neither has given us any miraculous results, but they
might be subtly helping on a microscopic level.  He's only had two
Enzyme-Aid tablets so far, so can't make a judgement there, but we tried
Seren-aid for 6 capsules and nothing helped.  These supposedly help to
breakdown gluten or casein after accidental ingestion.  I'll let you
know if the Enzyme-Aid starts to work.

In any case, thanks for the input.

Catherine in AZ