S., Congrats on the new baby girl! I am a pediatric RN, and mom and bfeeder of three, so i hope i can help.
Is it that baby won't sleep laying flat or she won't sleep when laid down. Remember, if you nurse, you are holding her a majority of the time she is awake and probably a lot of the time she is asleep. She may just be used to being held and we are warm, so the change between being held and being laid down is cold and wierd to her. Also a cool bed is strange, a hot water bottle laid in the bed until you lay her in there swaddled up will warm it up. Make sure the foods you are eating aren't giving her gas,(cabbage, lettuce, beans, etc) which might be more unconfortable lying flat. Also, go ahead and burp, some bfders do, some don't- maybe she needs it. You can prop her mattress in her bed (only a few inches, make sure she won't roll down the bed sideways) up by using a blanket or towel rolled up under the mattress itself. We do that in the hospital for sick kids, too. I doubt very much it's reflux, unless she is spitting up massive amounts of formula. I would guess if she were in the nursery she was probably propped up in the little basinette, too. Some people just do that as a rule. Be sure to wrap her up tight, too. They like that and it soothes her. Be sure to help yourself by trying to schedule her feeding as much as possible, Q2-3 is fine as long as she sleeps between and acts sleepy then wakes to feed. And, once this time of upset passes with the sleep problem, be sure to lay her down after she has fed and is trying to go to slep. She will learn that in her bed is where she goes when she is sleepy and she will become used to going to sleep in there. You would be suprised how much even at this age that they look at mobiles and such. There is nothing wrong with laying her in there a little groggy, talking to her a bit, giving a few nice pats to help her nod off. It develops good sleep habits you need with two this close together. My oldest two were 20 months apart, i feel your pain. I hope some of this might help. I doubt you need any medication, just maybe try a change or two and see how it works. It takes a few days to get things just right, but it is possible. SOunds as though baby is great other than the crying, right?! Good luck!