I just had to answer because I love the thread title. Not that I know that much about horse care.
My question would go to the cause. Are you sure they're eating the same foods, in the same quantities (more or less)? Maybe one is, er, getting more fiber than the other. I agree that you'd expect them both to be afflicted so I'd start to look at differences in diet, exercise, exposure to disease, etc. Or is one stressed more than the other?
Lots of thoughts off the top of my head, no solutions, I wish I could help more. Perhaps it'll be a sign of improvement if he gets the canters.