It could be a simple irritation from being so dirty; I'd just try to keep him cleaner; perhaps try buying some straw and putting that over his shavings, so that he's not 'totally' on wet all the time, but has a couple of layers. Even when a stall is clean all the time, if it's a dirt floor, and the horse is in it all the time, the floor just stays wet after a while. Not that the BO shouldn't be cleaning his stall, but you will still have to take extra precautions in managing his feet, even with his stall being clean, now. You could get something like Cut Heal Hoof Heal, to help prevent/heal thrush, if you suspect that it's starting.
As far as the skin problem, if it doesn't go away in a couple of days, I would call the vet again, and actually speak to him/her. Maybe take some photos of it in and show them to the vet, even, so they can get a visual of what you are talking about.
"The ideal horseman has the courage of a lion, the patience of a saint, and the hands of a woman..."