From what I saw at your house...my guess would be an internal parasite. Have you noticed any stringy white poop? Can't remember if you mentioned not noticing that while I was there. That being said, I'm pretty sure my diamond goby never had stringy poop that I noticed, and yet he never gained weight for a year and was always VERY skinny.
I treated the tank with Prazipro and he fattened up within weeks. I'd suggest trying a medicated food with dewormer to see if that helps, or treating with prazipro...which is fairly "reef safe". Read up on it before you make that decision; I'd probably go the medicated food route first though.