Somebody has blown her mind. You can try giving her a break but it sounds like she's actually responding to you so I'd continue on with the patience and hard work.
Alot of times they come back to you, I am a big "abused and neglected" person. My walking horse only took a couple years to come around to me although he's still terrified of men. Both of my QH's still have quirks. One is terrified of a longue whip. You have to move very slowly when picking it up and let him see it and keep it level with the ground. I can't even move it when it's on the ground and he's in the ring because somebody whipped him really badly. Ohter than that he has not that many issues, he does have the spook issue that you mentioned, but now, he comes back to me pretty quickly, He was a freshly gelded 4 year old when I got him. I've had him for about 5 years now. My older QH, has no respect for men to this day, I got him at three and he's 24 years old now. He no longer fears people, but he had been pushed past the point of fear into starvation and anger. He took longer to come around and still carries anger towards men.
The thing with these horses is that if you can hold on to your patience and work through everything, they are really really good horses, once they realize that you are there for them. They try so hard to make you proud. But my personal experiences took me years to bring them past their issues... It's not like in the movies where it only takes a few months! But it really sounds like you have come really far. Keep on working at it!
Oh... and I just re-read and saw your gate/fence issue. My older QH, he was locked in a stall for weeks at a time w/out food or water, he has JUST gotten to where he doesn't run me over to get out of a stall (He used to knowck the door down). He still will force his way out if he thinks he can get away with it. But I let him out 24/7, he has a dutch door and does not get locked in except for specific reasons (terrible weather like ice storms or if he's sick or hurt). Somethings they just don't get over. But they learn to deal.... You know?