With out knowing her past it's hard to say what's going on in that brain of hers. Just keep helping her for now and hopefully she'll grow out of them.

I know King didn't have a happy past and it took over a year for his REALLY bad dreams to go away (mostly... there was always that occasional one.)

Do you keep your place too warm at night? 19.5 - 20.5 C is usually about right for sleeping (for humans) 21 C is too warm though. Being too warm can cause bad dreams. I have no idea what proper sleeping temp is for dogs but i still imagine it would affect them.

Maybe let her sleep with a shirt you wore that day?