I first noticed symptoms in my horse when he was out in the field, standing around. He hasn’t been ridden for nearly 2 years and still head flicks. He is worse under stress - some days, simply catching him and bringing him to the stables will set it off. If head shaking is about mouth pain, caused by a bit, I would have thought that after this amount of time, it would have settled.
I think that my horse’s head shaking was triggered by an allergic reaction to something (in the environment, probably a grass, hay or straw variety), he is now very sensitive to it and small amounts can set him off. If i could put him in a sterile, sealed environment I could do some elimination tests, but its difficult to find one of them for a horse!