When you rule out pain, then you have to treat it just as a habit. I can tell you for an absolute fact that once a horse has cross-fired a lot, they become very comfortable with it and it can become their 'normal' lope, sometimes even when they not loping in a circle or through a turn. Most of the horses that do this are either very 'thick' heavy made horses that lack flexibility or do not possess great natural athletic ability. A horse bred for the barrels should have more agility than that.
I have had quite a few horses that had become very comfortable with cross-firing and I got them all to not do it or do it only occasionally. I was able to get all of them to stay true-leaded and only occasionally flop out their butts.
You can scold a horse and use negative reinforcement to stop the from cross-firing. I am so adamant about a horse staying correctly in lead that I make them 'fix' it from the very first time I put them in a round pen or on a longe line. I absolutely want them to know from the git-go that is not going to be accepted.
I always get after a horse and make them 'catch up' with the hind lead and never let them slow down, break stride and start over. I want this to hold over to riding and any horse that is going to be 'used' is going to have to stay 'in lead' to get anything done. Barrel horses, in particular, need to stay in lead because they cannot 'drive' away from a barrel to the next one if they flop out of lead behind. If you watch 'high level' futurity runs or big 'open' barrel events, you will see that every horse with a good time is staying in lead and bringing that inside hind leg way up underneath them so they can drive away hard from the barrel. You will also see many horses that flop out half way around a barrel. They NEVER do any good in placing. Is costs them too much time.
When I ride a horse, early on, I teach body control of all five parts of the horse. I want to be able to move a horse's hind end over when his head is also facing that same direction. To successfully barrel race at a medium to high level, you have to be able to teach full control of the horse's head, neck, shoulders, ribs (body) and hind end (hips). So, you have to do what you have to do to teach this horse NOT to flop his butt out. It has to have severe consequences. Every time he is allowed to do this without consequences, he thinks it is OK to do it.
I KNOW that you can stop them from doing it because I have done this many times. The longer you let him do it, the more difficult it will be to correct.
Always remember --
"Whatever you allow him to do is what you are training him to do!"
"The worst performance or behavior you accept (and do not interrupt or correct) is the best behavior you have any right to expect!"