I would do a lot of groundwork with her and spend as much time making her think I am the boss, not her, not the gelding. I have a mare that I bought a couple years ago and one day she started running away from me when we went to catch her in the pasture. Well, I did the usual thing of chasing and cornering, and food bribing. Each worked temporarily, but after a while they did not work anymore. I got to the point where I thought in my head, if she wants to run away and not listen to me, then we are gonna give her something to run from. The first day I had me and 3 others basically chase her around the pasture till it was not fun anymore. She got hot and sweaty and finally gave up. The next day I did the same thing with the plastic bag on a whip and chased her around until she gave up. Over a months time she went from taking an hour or more to catch to less than 5 minutes. In about 2 months all I had to do was walk out with a lead rope and she comes running to the gate now to see me. No treats, no bribing, no disrespect. She use to kick out and bite at me when she would run away, but all this has stopped since then. She would also walk ahead of me on the lead rope and try to run me over going into the barn and she has gotten over this, she needs a reminder sometimes, which I just take her back outside and we do it all over again until she gets it right. Over time, since she is new there, she will get better as long as you work with her on her manners. I would not seperate her from all the others, but when you are working with her try to get away from sight and sound of the other horses. Get her to focus on you, and only you, not the tree on the other side of the pasture.
One of my mini mares live in the stall with my mini stallion. It is a similiar situation, he is her rock. If I am not around and he is not around that poor mare is lost. I have it worked out with her so that she is happy all the time even when he is not around because she sees me as herd boss. If I am there and so is he, she will listen to me over him. She is definitely boss mare of all my horses but Buck is her protector.
Do not give up, it just takes a lot of time and groundwork to teach youngin's good manners. If she kicks out at you and runs away, give her something to run away from. Chase her until she tires out and gives up, that is what a lead mare would do to her for that kind of disrespect. You will know when she has had enough of being chased, because no matter what you do she will not run away anymore. In time she will come running when she sees you coming to the pasture. It is not fun being kicked, trust me I know! It hurts!
If you have any questions feel free to PM me and I can answer them.
You know how to make a miniature horse even smaller? Leave them in the dryer a little longer!
"Don't ever regret something that once made you smile"