I got a male BC pup that we picked up when he was about 4 months old and had alot of problems with him doing what it sounds like your pup is doing. Not sure what had caused it, but he did and still does act nervous when things don't seem right with his way of thinking.
The first thing is, never get mad at the pup, then tell him to come. It doesn't take BC's very long to figure something out. Second, some of these dogs you have to be real careful how you reprimand them.
When I am getting manners on my pups, and they get out of hand or don't want to listen, I will get them by the collar and press them down on their side. Not forcefully, and not on their back as if they are giving in. And then if they want to try and run away from you, go catch 'em and do it again. Work on sit and down and all the other manner commands.
I have only been breeding BC's for about four years, but everyone I talk to in the trial ring, breeding business, etc, is that you have to teach the pup manners and to like you.
The male I referenced at the beginning of my post is an excellent working dog and is great to be around, but if he has the slightest sense he's done wrong, he's takes off and is real reluctant to come back, but he does and you sort of have to act like nothing happened and go on. It sounds to me that your pup might be at the point that she thinks she is in trouble when you call her. So you just need to be patient and work with her to show her that she can trust you.
And do put her on a line and make her heel and stay with you. It's not going to hurt her one bit to be on a line and learn its okay to be with you. Put her on a line, make her sit, walk away with the rope in your hand, stop and call her to you. If she doesn't, wait a few seconds, say her name and tug the rope a little bit. She'll figure it out after a bit. Just be patient.
I love talking working dogs, training, everything about cattle working BC's. Everybody feel free to PM me or email and maybe we can all bounce ideas off each other.