I agree with Roger here. Both our kids have reflux, but that is being medicated. Our oldest even had it much worse than the youngest, and they both take the same medication. Nevertheless, the oldest is a very good sleeper. He's been sleeping though the night since he was a few months old (apart from the occasional exceptions of course). The youngest, who is now 16 months old, is still a bad sleeper. She'll usually wake up once or twice per night, usually between 4 and 5 am. Sometimes we can suss her with a pacifier (dipped in honey - I know it's not the best thing to do, but it's the only thing that works, trust me we've tried everything else), but usually she doesn't stop until I bring her a bottle. Which I usually end up doing, even though I don't want to make a habit of it, but letting her whine isn't an option here since she'll wake up her brother then.
I doubt it's also a case of her being hungry. She eats more than her brother does. The only thing we can think of is that a lot of the times, she just decides it's time for a little "me time" with mommy and/or daddy, so she'll start to whine - even though it's the middle of the night... BTW, that's also a reason why we believe it's just a bad habit of hers: she doesn't cry in the true sense of the word: she just whines and eventually starts yelling if we don't respond quickly enough to her liking.