You're right..acid reflux and a milk intolerance are 2 different things. Both of my kids have/had reflux and here's what I learned from our pediatrician who also specializes in gastrointestinial disorders at Hopkins.
There's a muscle in their esophagus called a sphincter that acts as like a flap. It opens when food goes down and shuts when there's nothing to go down. It's immature in babies up until 8 or 9 months and just kinda flops around willy nilly so the acid in their stomach comes back up (as spit up), it burns their throat. Hence the term "acid reflux". The medication that our kids have been on, Axid, just neutralizes the acid. It doesn't prevent the spit up from coming up. Others like Prevacid and Zantac do other things, but have different side effects in babies. Axid has none and is very safe.
The reflux DEFINITELY ties into the type of formula they're on. The partially broken down proteins are easier for them to process and the lactose content (or lack there of) is important. The less lactose, the less irritating it is to their stomach lining which keeps the acid from over-producing.
Three months is still pretty young to be switching formulas and I don't know that you want to find out the hard way that she can't tolerate another type. It can be pretty nasty...long nights, super cranky baby-which you've probably already experienced! My vote, and what our pediatrician recommended to us, was to keep them on the same formula for at least 6 months. I never took the chance with our first son. He was on the Gentlease until he didn't drink formula anymore...at 11 months.