From what I've been reading your Alk is a bit high and Ca is a bit low for running pellets. This alone shouldn't be causing the issues though. Are you feeding everything heavily? This is important when using pellets as they strip it all out quite quickly. Is your reactor a recirculating type? Too much flow through the reactor can introduce too much of the mulm they talk about. It might be worth adjusting your Alk and Ca, feeding heavy, and turning down your reactor's output for a while and see what happens.
I too have started pellets recently and did noticed some coral decline initially. I converted my reactor to a recirculating type and started feeding more fish food and more coral food (reef roids) and things turned around quickly.
I'm no expert, just sharing some info I've read and some things I've tried.
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