My TB Grey mare had scratches for many years. I tried everything recommended by my regular vet, a homeopathic vet, everything I found online and in magazines. She spent 5 days at Littleton Large (for a different issue) and they treated her scratches as well. Looked good for a few days after I brought her home. My vet even had CSU do a culture and we followed their instructions for months to no avail.
Veterycin VF (veterinary formula) gel spray was my lifesaver. Spray on twice a day until results are seen (scabs fall off and skin looks healthy). I then continued to use it once a day. The best part is that it is not irritating to the horse! No more scrubbing, no taking your life in your hands trying to work on their sore feet. The VF formula has more active ingredients. Use the gel as the liquid spray is too wasteful. Each case is different, GOOD LUCK