Usually the recommendations are to eat gluten (two slices of bread per day for an adult) for six weeks prior to any testing. If you don't stick to the guidelines a negative result won't tell you anything further. What did the doctor say about removing gluten before the test?
It sounds like you are pretty certain that gluten is a problem. How likely is it that he might have Coeliac Disease?

I'll flick this reply off into a new thread.

Not certain that gluten is a problem at all, no history of Coeliac in family (diagnosed anyway). He has only been off gluten since Thursday and his nappies haven't stabilised at all. Dr advised to stay on it until testing but I think I am going to give him a full week/10 days off it to see if nappies improve (plus a dose of probiotics over that period) and then go back on it - and that will still be 6 weeks before the testing anyway.

Thanks for your comments

Your plan sounds good to me.
I hope you can find the cause for the messy nappies. Is he formula or breastfed? Do the bowel motions cause a rash on his bottom?

On Neocate (what he drinks of it - which = 80mls per day) The rest of his required quota goes into his solids. No rash from motions either - but then I figure the losec reduces the acid out the bottom end too.

Neocate can cause unusual bowel motions. Is it just that? Dark green in colour I believe. What is the smell like? Sorry - too much information! Losec can also alter the bowel motions causing diarrhoea or constipation. Do you think the bowel motions are causing any weight gain problems? Might be a bit hard to know if he doesn't have much Neocate.
My experience is that if the bowel motions are runny or messy due to a food allergy they burn the bottom or at least cause a horrible rash possibly with thrush. Gem was on a good dose of Losec at one year and gluten still went straight through causing a bright red bottom where it touched that blistered and got infected whatever I put on it. My eldest was the same but not on Losec and toilet trained herself early before age two years because of the pain. We didn't work out her problems with gluten until three years after we worked out Gem's and there is eight years between them. Poor kid.
Still good to get the testing done if he is having other tests. It may not be affecting his bowels but could be affecting reflux, skin or something else if it is an issue.