Maybe she is having nightmares. My son started having that problem at 18 months and I couldn't figure out what to do until a friend of mine suggested taking him off sugar at night and other possible food sensitivities. It turned out to be a combination of things I took him off sugar at night and it made a HUGE difference and then I tried taking him off milk and it stopped completely with only rare times that he wakes up anymore and almost always it's because he ate something sugary too close to bedtime. It may not be the answer for you but it's certainly worth trying out.
Good luck, I hope those sleepless nights end very soon.