With DD (and yes, I meant failure to thrive.. she looked like a starving African child with the big belly and the gaunt face), we also had a paediatric dietician, who had us on the Homeward HENS (google it) program, which is what they tube feed kids, but we gave it orally to avoid needing a nasal gastric tube. You can add it to food (there is powder, or a great liquid one (name has escaped me)) that you can mix into any food they will eat, and it is great for weight gain. I think its 100 cal per 100 ml, so you get their calorie intake up.

A paed dietician might be able to come up with some ideas to try.

Have you done a stool test to look at anything that might be coming up? Ours came up blank but it was good to eliminate everything.