Hi Shelley,
I just want to share my story in case it helps. My son had reflux and was on Zantac as an infant. He also had trouble with always being very congested - both of which contributed to his sleep issues (he was never a good napper either). At four months old, he had never slept longer than a two hour stretch at night. He would wake sounding congested, I would steam him, suction his nose, feed him, rock him, etc. At his four month check-up our pediatrician said it was time to get him to sleep through the night. He suggested Dr. Ferber's method (also known as "cry it out")and gave me a handout and explained what I needed to do. He said it would likely take about a week and then he would be sleeping through the night.
WELL...I let him cry every night when I put him to bed and every time he woke up (There is a method to it, so it's not cruel and you don't just shut the door and let them cry all night. And, no more night time diaper changes.)
And cry he did! After three weeks, it still had not worked, so I gave up and he went back to getting him, feeding him, comfoting him EVERY TWO HOURS (I was also working full-time, so needless to say, I was a sleep-deprived mess.)
Then, at his six month check-up, the ped. was dismayed that he still was not sleeping through the night and pretty much "insisted" that we try again and not give up becasue he feels sleeping through the night is crucial for a child's well being and development. He said even with the congestion, my son could learn to sleep through it. So, I tried again. One week...four weeks...six weeks. He started sleeping longer around week four, by week six was waking only once a night, and after eight weeks he was sleeping for 12 hours straight. That was almost seven months ago and he has been slepign ever since. He still onlly naps for 30-45 minutes during the day, but with his 12 hours at night, that is enough for him.
My point is, every baby is different and some don't respond as quickly as the "normal" baby. For my son it took two whole months. My suggestion is to follow the program you choose (Ferber, Sleep Easy, etc.) to a T and keep it up until it works. I know it can be difficult, but hang in there and stick with the program.
Since your son's reflux is managed by Prevacid, I would agree with your doctor that he is not in pain.
My 2.5 year old also had a sleep problem recently and we took a different approach becasue he is older, verbal, and not in a crib. But with your little guy being only 12 months, he is still at a good age for a program like the Ferber method, or whichever method you are comfortable with.