I had GERD before going paleo, but it got worse when I started - I suspect this is because I was using acid blockers, and having gone off of them, going Paleo allowed the proper minerals to be absorbed (zinc, magnesium, potassium, etc.) which produced more acid reflux.
However, the GERD did not go away until I took out all dairy about a month later.
So you'll have to find what triggers it. For me, wheat causes me the runs, but then immediately, acid reflux comes back at night. If I consume a bit of dairy (amount varies, but typically cheese, even raw milk cheese) triggers it. So far the only dairy that doesn't cause it is goat kefir/cheese.
I don't think it's lactose related for me, due to the timing, plus there's not much left after fermentation, so it's something in the proteins, likely the casein. As usual, you're your own n=1 and YMMV.
It might be the coffee, it might be the brand of coffee, or it might be what you put in it. Who knows, maybe they used the same grinder they use for wheat flour to grind your coffee if you picked up some low quality stuff.