J.,
Try to aim for calorie dense foods. It's difficult to do with baby food, because if you read the jar, there is so much water that each serving has very few calories. i know it can get time consuming and inconvenient, but making baby food for her may help, because you can keep more of the water out. Take boiled or steamed vegetables and fruit, and puree it in a food processor. If you can get it nice and smooth, you won't need to water it down, and she'll get more actual food per ounce she eats. Also, use formula instead of water to mix her cereal. It addes calories, and every little bit helps.
I have to say that your daughter is on the small side, but is between 10 and 25 percentile for her age in weight. It is usually under 10 that they worry about being "underweight".
You said she lost a lot of weight at one time because of throwing up due to reflux. Has she begun to gain back again? If she's gaining an appropriate amount per month or between doc visits now, then it is just an issue of her catching up for the lost time. If she is gaining from month to month, then I wouldn't worry too much about it, she'll make up the lost ground over the next year or so. If she is eating and holding things down okay, and still not gaining, then it is time to talk about other options with your ped.