This may not be what you're experiencing, but I get a burny stomach (no actual reflux unless it gets out of hand) when I have a bacterial overgrowth (unbalanced gut flora). I think Chris Kresser's site explains it best, but basically when you have an overgrowth, it causes gas and abdominal pressure and that backs the acid up in your stomach. The hidden causes of heartburn and GERD
I already take probiotics daily, but if I've been bad on my diet particularly with carbs/sugar (such as binging on Halloween candy, doh) the excess sugars/carbs feed the bad bacteria and I have to take extra probiotics/add in things like kefir, fermented foods, etc. to balance it back out. I'm working on getting rid of a flare right now.