Probiotics at Whole Foods are in their own section, usually in the same area as vitamins and supplements, in a refrigerated case, as probiotics generally need to be kept cold as they're actually live organisms. There are capsules for adults, chewables for kids, and a variety of powders good for dissolving in liquids or mixing in other foods, and some are specifically made for infants/babies.
Does the GentlEase have any soy in it at all? I know that soy intolerance isn't unusual, and if you have soy in your diet but there isn't any in the formula, that might be the trigger. Soy is REALLY REALLY hard to avoid, but it IS possible. I'm not sure if the symptoms would be related, but it might not hurt to check into it; one of my kids' sitters is intolerant of soy and the soy formula they gave her as a baby was how they found out.

Also, depending on which meds your LO is taking for reflux, they may or may not have anyhting to do with the actual throwing up. Zantac, for example, reduces acid but does NOT inhibit the muscular reflux action, while other meds (I forget which ones, sorry, but we were Zantac users here) do NOT reduce the acid but DO inhibit the throwing up.
When I pumped, I did notice changes in the composition of my milk depending on when it was pumped and sometimes around a growth spurt., but most times I pumped a full feed there was a decent amount of fat. Are you yourself getting good helpings of GOOD fats daily? Butter, olive oil, dark meat chicken, full-fat milk and yogurt, oh, and coconut oil (also available at Whole Foods), and flaxseed oil and fish oil - ALL of these are good fats.
That's all I can think of at the moment, but I've been checking back to this thread. Keep us posted.