Have you considered looking for a new farrier. You say that the horse gets worse each time he's done - is it possible that the farrier is part of the problem?
Does he shoe the horse in a barn where the flies tend to not hang out so much?
See, I always get in trouble for making a short story long, but when I try to make it short, I end up having to go back and explain. Lol
Here goes: I took him to a farrier in September after I got him. I had used that farrier for over a year with all my other horses. He shod DJ for the first 3 times. It was a couple days before my appointment and I needed him done sooner, so I tried to get him to take him in sooner. He couldn't. The guy up the road from him could, so I took him there for his 4th shoeing a week ago. In the mean time, I had won a gift certificate from a highly respected, VERY EXPENSIVE farrier. I had him out to do one of my horses ('cause that's all the $100 certificate would cover) and asked him to check the work the Amish guy did. He said the only thing he would change would be that DJ needed a bigger set of shoes, and shorter heel. I took my third horse back to the Amish guy since the gift certificate only covered one horse, and while I was there, I asked him to redo DJ and asked him to shoe Skunk the way the high dollar farrier suggested and showed him the job he had done on Scooby and said I wanted them all like that. So that is why he got the 5th shoeing only one week after the 4th. I am going to let this other Amish guy start shoeing my horses now, but the point is, DJ acted the same for both.
Could it be the farriers? Sure! I just doubt it is though. They are both extremely patient and gentle, but firm, with him.
And it's in an enclosed large garage type area. Honestly, there is NOWHERE around here where the flies don't hang out!! :(