Join Date: Dec 2011
Location: Washington State
In addition to checking his sheath and cleaning his dock, worm him with a fairly high dose of Ivermectin - he might have pin worms, and those don't necessarily show up in a fecal count since they live burrowed into the horse's intestines. Also, check to see if his anus is dry and cracked - if it is, it'll itch like mad and he'll be rubbing to try and relieve that. But ask your vet what would be safe to use to moisturize that, since it's a fairly delicate area. ;)
After you fix the cause of the itching, make sure to keep his dock clean and moisturized with something that won't leave behind a lot of residue - I've heard that coconut oil works really well and actually soaks in without leaving behind any gunk. Then you just need to keep his back end itch-free and give the hair time to grow out.