I'm glad things have improved, it sounds like he's doing great! I wonder if maybe the rubbing might aggravate his reflux as well? Tyler didn't have reflux, but he hated any kind of patting or rubbing. He did much better when I just laid my hand on his chest, back, or thigh. I kept up the shhh, but I think the patting and rubbing just stimulated him for some reason.
Sometimes, though, they just have weird days every so often, then go back to normal before you know it. Hopefully that's all it is...keep us posted!