What are you doing to make her jump though with your hands is what I am wondering? Do you do some sort of "get away" motion with them to make her move off?
You need to keep your hands quiet and calm when dealing with horses. This horse may just be more reactive too, and needs even more low key movements.
May also be that in stall, she does not see as well and is more easily startled.
She can end up with poll fever if you aren't careful and then you will have a mess. And if she hit head hard enough to make her legs shake, I would be watching the places where she has hit head very carefully too.
I don't know about putting anything on the beams/rafters as if she can get to it, she will pull it off.
But whatever you are doing or is going on to make her startle, you need to identify it and quit it.
Might paint board lighter color?
Horses make me a better person.