Only just spotted this. Shows you what notice I take!
I've been in exactly that position when my own Tilly went missing a couple of years back. I also work with ferals for CP.
A cat's memory (from my personal experience) is around 3 months. I've seen this myself settling ferals into new environments and also observing my own cat adjust back from feral living to being a pet again. After 3 months they seem to forget certain things about their past or where they lived. My Tilly was missing for about that 3 month mark and she too was a very different cat at first when she got home. Her body language and behaviour was very feral like at first. I dare say give it another couple of months and it would have been a great deal worse.
The first days adjusting back to her normal life, maybe even up to a couple of weeks, Tilly did seem to suffer nightmares. She would cry out in her sleep and wake up looking very scared. I didn't know if she was scared about what she went through before being found, or whether she was scared because she didn't know where she was. I don't like to think too much about what it was like for her - she's an older cat, only has a couple of teeth left and it was mid winter like it is now. Certainly the ordeal was enough to greatly upset her and it was like recovering from a trauma.
I could tell this was a very disturbing and unsettling period for her so helping her recover did require some thinking. The way I handled it was to carry as normal around her, perhaps pausing for some quite chats and lots of fusses. Slowly, her brain started to recognise certain things around her and you could see the dejavous flicking across her face.
My advice is to follow the excellent tips Liz has given. Feliway or Zyklene will help I am sure. But in order for your puss to remember her previous life, you need to carry on your daily living around her in a way that was familiar to her before. Sadly it sounds to me as if things have got so emotional that you are sending out 'signals' which she's reacting to. Anxiety travels through your shoes, across the floor and into the paws! Forget she's come back if it helps... put her food down, tray down and let her get on with it. Let her explore and get her memory back in a way and at a pace that she feels comfortable with.
At CP we are used to working with long terms strays a lot. Some of them take longer to come round than others. Patience is the key. But we have never known a case of a cat who has once had an established domestic life before straying that didn't adjust back to it eventually... indeed very many of them are so grateful for the easy life again they turn into great big cuddle monsters.