Maybe your baby is just a mover at night. My son will go from the bottom of his crib to the top and he whines and fusses periodically too. I have learned to let him fuss for a couple of minutes (not full blown cry but fuss) and I find he goes right back to sleep. Sometimes he'll lay there and talk to himself for 10 minutes the go back to sleep.
At first I would go into his room and move him back to where I first layed him down and that would wake him up, so there we are "party time" at 2:00am.
I'm not sure about the reflux thing. I'd say if she were truly uncomfortable, she'd do more than whine.
Maybe you should find a new doc if your not happy.