Do you use anything that might upset his skin? Straight arrow makes a fungal and dry skin shampoo maybe that would help along with some coconut or olive oil.
Maybe it's a fungus? If you can.. try to rinse off sweat( if weather permits) after every ride and then apply MTG to the area.
You can put some vegetable oil in his food. It makes the skin more supple and hair healthy and shiny!
I use dandruff shampoo and melt some coconut oil and rub it over my horses coat. I also mix it in with fly spray so it gets applied in between baths. Some people also put oil into feeds.