She probably needs systemic antibiotics to clear it up. You need to contact your vet for advice. Topical treatments can only do so much. If the infection is deeper, they don't work. A horse this vulnerable has already had this infection in the past so that the skin layers are already " seeded "with the bacteria (anaerobic dermatophilus congolensis) and it manifests every time wet conditions render the skin vulnerable. You probably need to treat it both systemically and topically to get it under control, which requires your vet to prescribe the antibiotics.
Add....if you are doing topical treatment, I advise you to use 0.9% isotonic saline available at any drug store. Soak the scabs and gently remove them when they soften. Then use saline-soaked cotton to clean the open sores. That is all you need to do. The salt in the saline will dehydrate and kill the bacteria, and exposure to air will prevent further bacterial growth, since the bacteria are anaerobic and thrive when there is no oxygen present.
For rapid healing, there is a spray-on product called Vetericyn that is an ionized saline. It also comes in a hydrogel form. It is FDA approved and cuts healing time by over half. It won't harm healthy tissue the way Listerine or iodine or other commonly recommended products do, but it will enhance the body's own healing capabilities. It has passed the rigid and extensive testing required for FDA approval. Isotonic (0.9%) saline will do the job and is much less expensive, but the Vetericyn is that much better and will hasten the process. I would still use regular isotonic saline to soak and remove the scabs, and use the Vetericyn to treat the open sores after the scabs are removed. If the infection is isolated to the outer skin layers, then this treatment may be all that is needed. Again, if the infection is deep, it may require systemic antibiotic treatment.
http://www.vetericyn.com/benefits/equine.php
PS....Rain rot is not a fungus infection.....it is a bacterial infection. I know the internet is full of misinformation and many sites refer to it as a fungal infection, but it is not. Antifungals do not treat dermatophilus congolensis infections because antifungals treat fungi...not bacteria.