Sorry to hijack OP - I seem to be doing a lot of it this week
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Submarine, your post struck a cord with me. My ds1 has always been very lean and we struggle to get and keep weight on him. He tested negative for coeliacs - although was ill with d&v bug just before the test and hardly ate for 10 days, so paed thought that could have affected the result and recommended he was kept gf just in case. He did gain weight initially when he went gf, but then suddenly started to lose it again for no apparent reason. It has taken over a year for him to gain back the weight, with no gain at all for the first 6-7 months of that.
The reason your post struck me, was that the paed has being running some blood tests to check for various things and the three things that came up as anomalous were raised levels of B12, protein and eosinophils. (Worth pointing out here that he is a vegetarian, so would normally be expected to have low B12.)
Paed didn't have a clue what these results might represent and put us on a 6 monthly monitoring appointment whilst awaiting stool sample/enzyme results that have since come back as normal. Since that appointment, ds has very slowly regained the weight he had lost (so he now weighs about the same as he did in September 2010 give or take a pound) and we are due back at the paed's in May, although he was making noises that suggested if the stool samples were normal he would discharge at the next appointment.
Does this sound like it could be something similar to your ds or am I way off the mark? Its so frustrating not being able to get to the bottom of this weight problem, especially as our paed is coasting to retirement and wasn't concerned because ds was clinging to the 2nd centile for weight, so not under the red flag - iyswim. (He is now between the 2nd and 9th centiles, but despite being tiny eats twice what anyone else in the family does - including his father and has only gained weight from us making a big conscious effort to feed him up eg big portions, high calorie foods, 2nd and 3rd helpings etc.)
Again - sorry for the hijack OP, Submarine's post just jumped off the page at me.