Ben's mom, it took our Ben some time to finally even out after 14 weeks of malnourishment due to needing enzymes and being undiagnosed. When they do not have enzymes for so long the gut is inflammed and never had a chance to build the proper flora to aid in digestion. We breastfed and supplemented the predigested formula at first. They kept wanting up to slam calories into him, but honestly the higher we went in calories the worse off he was. He could only tolerate a little bit of the stuff and only at 22 calories max. If we went up his poops went south no matter how many enzymes we gave. I think there is a point where too much fat and protein from formula will just taxed their tiny recovering systems and it show no benefits (my nutritionist actually agreed with this theory...I asked why they do it and she said she wasn't sure). The best thing we did was add a probiotic (acidophilus) to his applesauce everyday. Culterelle is good but we switched to KidDophilus because he can't handle any dairy. THis helped build the gut flora and reduce inflammation. After about 6-8 weeks of helping the gut to heal, he gained. We slowly weaned off the formula and he eventually kept climbing the charts. When he was introduced to solids around 6 months, we would add a tiny bit of MCT (melted virgin coconut oil is also great and is medium chain fats; it also helps gut flora) to his rice cereal and fruits/veggies, but we went really slow so we could adjust enzymes if needed. Too much oil will also go right through if the gut can't handle it.
Perhaps a strategy to discuss with them is to work on establishing gut flora with probiotics, reducing calories (getting the extra MCT out for a short time) until some absorption is seen (stools begin to normalize). Then if he can handle it, slowly go up to maybe 24 cal. This weight thing isn't an over night thing and in my experience takes many months for all the systems to normalize from being malnourished.
Hang in there. Slow and steady does it.