One other thing that could be a possibility is parasites?
In my reading about health for humans I've read of stories that some parasites will keep people fat. Once they got rid of those parasites the weight began dropping off. To me it seemed like a parasite that lived in the blood. But don't quote me cus it's just something I passed over 10 months ago while reading. And I didn't do much reading on it.
And I wouldn't have a clue if this would also pertain to horses. But if there's some that cause humans to retain fat then I don't see why there wouldn't be some that would do the same to animals.
And I also wouldn't know if it's a parasite that could be found doing a stool test or not.
I'm not much help. But everyone else offered great suggestions and this is one that I could think of. LOL
If the horse is on pasture too then you may consider reading www.safergrass.org
The times of day, temperatures, rainfall or drought all affect the nutritional quality of grass.
Shoot.... I just thought of another thing I learned about a couple of weeks ago. Thyroid issues can cause a horse to be fat too. And the thyroid has two halves, one half could be over active and the other half could be under active. And in such a scenario most common tests will show that the thyroid is perfectly fine when it is not.
There's an accupressure point on the neck I believe that will allow you to know if it's the thyroid that's causing the horse to stay fat.