i agree also that you should keep cuddling.

my ds does this every now and then. It seems to be a couple of nights per month that he will wake up screaming and I go in and cuddle him or take him into our bed to sleep and he is fine. I'm sure your dd just wants that reasurance that you are there for her, perhaps she is having a bad dream and wants mummy to comfort her. Our ds hasn't formed any type of habit from me going in to comfort him or him sleeping in our bed, so i'm guessing it wouldn't be an issue with your dd.

Your doing a great job, i know it does get very tiring, but you are doing well, and if you keep doing what you are doing (cuddling dd) then i think it will resolve itself.