If you suspect celiac disease a blood panel for it would be the best option. This article might be helpful. It breaks down each type of test, and what a positive results means in terms of the probability that you might have celiac disease. One test that always needs to be done is the IgA Levels/Deficiency Test (often called "Total IGA") because some people are naturally IGA deficient, and if this is the case, then certain blood tests for celiac disease might be false-negative, and other types of tests need to be done to make an accurate diagnosis. The article includes the "Mayo Clinic Protocol," which is the best overall protocol for results to be ~98% accurate.    

Your only resort would seem to be directly contacting the manufacturer and ask some pointed questions about CC . . . and hope you get some straight answers. You are probably already aware of this but the label "Gluten Free" does not necessarily equate to zero gluten. "Gluten Free" is a standard established by the FDA whereby a product can use that label as long as it does not contain an amount of gluten exceeding 20 ppm. There is also "Certified Gluten Free" which is a third party certifying standard signifying that the product does not exceed 10 ppm. There are limits to detection technology much below that.    

It may be naturally gluten-free but I worry about cross contamination as my kiddo has had bad reactions if things aren't actually gluten free.

They will have to put him back on gluten in order to get accurate tests results, so all the progress may be lost for a while. My grandson was 2 1/2 years old when he, his father, and his mother, were diagnosed.  He was not even on the chart for height or weight and had not been on the chart since he was 12 months old.  The first month he went gluten free he gained 6 pounds and grew an inch.  Unfortunately, he missed a whole lot of opportunity to grow in those first years.  He remained the smallest, skinniest kid in the class until high school when he clawed his way into the middle row for pictures.  He is 20 and topped out at 5 ft 6 inches.  His mother is 5'7 in a family where everyone is 6 feet tall or more.   His younger brother was 7 months old when he was diagnosed.  At 18 he is 6ft tall.  Best to catch it as early as possible.

Maybe you picked up a little intestinal virus? Maybe some ingredient in the gluten free processed foods you've been consuming is causing this. In order to simulate the texture that wheat provides, a lot of gluten free products contain ingredients that may cause digestive distress. Xanthan gum and similar polysaccharides are among the chief offenders.