I've now and then had skin issues with my horses as well. Very frustrating!
Usually when there's hair loss, it's because they're itchy and rubbing the area. You've ruled out lice, and taking a sample to the vet as the next step was an excellent decision. I'm sure the vet will be able to tell you exactly what is is and how to treat it.
In my experience, there were two separate reasons: the first time, it was "rain rot", otherwise known as a fungal infection of the skin due to long-term moisture. The rain sheet I kept on him turned out to be not very breathable, so when he ran around in the pasture the sweat would never dry out. Taking off the blanket, a couple baths with anti-fungal shampoo, and the new spring sunshine took care of it.
This might be what's troubling your horse, since you've experienced this before coming out of winter - and this past winter has been wetter than usual.
The second time, my gelding was losing hair out of his tail, due to it itching so he would rub it on his stall walls, fenceposts, etc. It turned out he needed his sheath cleaned. Funny how a dirty sheath can make then rub their tail, but a good sheath cleaning fixed it.
As for nutritional deficiency, it sounds like you're doing everything right, except that selenium deficiency can cause hair loss. For grain, are you feeding plain grain like oats or COB, or more of a complete feed that includes vitamins such as selenium? I'm in WA, you're nearby in MT, and the Northwest area in general is deficient in selenium, so there's not enough of it in hay that's grown here (even though everything else about our hay is top quality.)
So, I feed Northwest Horse Supplement, which is made here to give the right vitamins for horses in our area. It's not easy to find - my local TS doesn't have it, but Coastal has it - I'm not sure if you have Coastal in your area. Maybe google their website, or Northwest Horse Supplement's website? It's like $90 for a 50# bag, but that lasts me about 8 months for two horses. You add 2-4 oz to each horse's daily grain, depending on what other grain you're feeding.
I would say, if the sample you're sending to the vet is definite about what's wrong, that's great and they will tell you what to do. If it's inconclusive or questionable, and you've ruled out a fungal infection, try a supplement with extra selenium.
Good luck to you, I'm sure you'll solve this problem!