Mud Fever or scratches can be a nightmare!!
The virus is able to live in the dirt for ages, i would try to see that your horse has his own paddock to avoid contamination.
Horses with white legs generally are more prone to this. Also high sugar grains can become a source of the persisting problem, but not the cause.
Washing legs daily with a anti-fungal wash and apply a anti fungal cream religiously!!!!!
Generally with mud fever there will be swelling in the local area as well.
Otherwise it's just a fungus and you should probably try washing your horse boots on a more consistant basis to avoid build up of sweat and dirt and try washing legs after workouts to help keep it under control.