13 month old daughter will not sleep

1. We had a great time on a vacation a month back. Radha, then an year old, slept really well during the vacation. Once we got back on July 19, we tried to reset her rhythm by following a plan – we would let her cry for 15 minutes and then go pat her – so she would eventually fall asleep on her own. This plan had worked for us when Radha was 6 months old. The plan did not work this time. She would cry so hard that next morning, she would have a cold and a runny nose. So, we would have to discontinue the plan. This pattern went on for several weeks and we never had a peaceful night after that.
2. On July 26, we had her vaccinated. I hope the effects of that is gone by now. I held her in my arms for a few nights – helped her to sleep
3. Three weeks later, she is sleeping next to me every night. Even then, she wakes up several times (every 90 minutes on average).
o We give her water, pacifier, etc. and it calms her most of the time.
o Between 2 to 5 in the morning, I also have to give her milk for her to stop crying.
o The strangest part is that almost once a night at different times, she cries uncontrollably for no good reason. Milk, Pacifier, Water, Holding her, rocking her ... nothing calms her. She has her eyes open and she does recognize us. But, she cries like she in lot of pain. She does not have a dirty diaper or fever. This crying lasts for an hour sometimes. Neither parent is able to console her.
4. She eats everything – cows milk, fruits (cherries, avocado), wheat bread, cottage cheese, etc. Good appetite.
5. During the day, she is in good spirits.