Saddlebag - You are absolutely correct, I got her at 7 years old with no history except for the place I got her from, where she was kept outside 24/7 with only a two walled shed with a roof. She learned to love her stall quickly in the small 2 stall barn. I think you're right, she likes to be in a secure place - but the big barn is scary.
You're also right it's a nasty habit of mine to be rubbing her and chatting at her all the time.
I do use scratching as more positive reinforcement, not so much as a 'good job' though. I use it more so she connects things she once thought were scary with things that bring her pleasure. For instance - she was horrified of my white bedding bags, but sometimes I need to add bedding while she's in her stall. So I turned it into a game, when the bedding bag was touching her she would get a good belly rub. Now when she sees me coming with a bedding bag she comes running. :P
I agree with the smile part - I find laughing and smiling a lot seriously helps the situation - lets the nerves out!
And Luv- I try to avoid using treats as anything other than a random gift she gets every once in a while for no reason. When there's food around she gets so distracted by trying to get food we don't get anything accomplished. BUT in a couple weeks when I need to get her on a trailer we will be using food and her best pony friend who loads real well to bribe her on. I don't have a trailer to train her the right way to be comfortable with one. But I also believe trailering may be one thing she actually knows how to do - she was born in Canada (as far as I know) and trucked auction to auction her whole life.
Thanks so much everyone!