I thought that maybe she has had some trouble with her ears at some point. Yes, it is possible for a horse to get ear mites. They can be treated topically with a miticide. I always try to look for a physical reason for a horse's behavior problems. If you are having trouble working with your veterinarian on this problem, you may need the help of an entomologist from a local university.
Ear mites are rare however.
More likely this horse has been ear twitched. This is a control method where the ear is grabbed and twisted to make the horse submissive. The immediate affect is the same as a standard lip twitch, the long term effect is that you can't touch their ears. Try slowly working your way up the horse's neck and approaching the ear from the outside. With ALOT of time and patients, you can work up his confidence enough to let you touch them.