I've posted a few times around cross-contamination and cross-reactive foods, and the uncertainty around cross contamination.
I've been to a dietician, and still on waiting list for NHS GI/dietician, but the theory that lectins may be behind a lot of the problem has proved an interesting exercise.
Lectins are a protein in a lot of plant-based foods, seeds, nuts and eggs. They should not cause problems and have health benefits, but for some folk, particularly those with a damaged GI tract from things like coeliac, they can cause problems/autoimmune response.
It's a theory that seems to be panning out for me, in addition to the suspicion that sugar is also kicking off a reaction.
The upshot is a very very limited diet and a lot of weight lose. Still haven't sorted out what's ok/not ok, and being caught out every other day, but I seem to be on the correct route with this. It's not an easy solution but the consequences/alternative is a lot of pain/inflammation/increased damage.
So, for anyone who is similarly struggling with their strict GF diet not fixing the problem/still causing problems, I would recommend having a look at lectins as a possible cause in addition to coeliac.
I do still think a lot of GF labelled foods have been part of this issue, and the low level gluten/cross contamination has maintained a level of damage which has allowed lectins to become an issue, so I'm strictly avoiding all GF labelled foods also.