I honestly and truly believe, after battling for the last 3 years with the horse trailer from hell, that certain things "surpass" a training issue with horses. My Arab mare has ALWAYS loaded, and loaded good - in 2 horse WW trailers and big open stock trailers. She adores trailer rides, she'll practically run you over to jump in.
Enter my 2 horse trailer and the ONLY way she'd get in on anything less then pain of death is if I removed the partition for her to travel alone. Anytime we went somewhere, she'd load fine at home, realize it was the hell trailer, and promptly REFUSE to get back in when it was time to leave. I've had cowboys forcibly pick her up and PLACE her in the trailer before.
This is a horse that has virtually flawless ground manners, lunge manners and any other types of manners. This is a horse that will forge ANY terrain I ask her to on trust alone. And this horse simply said "screw you and the horse you rode in on" when I asked her to endure one more ride in the hell trailer.
We encountered this with all our horses, and every last single one of them jumps no problem into any other trailer I bring around. I truly believe that some trailers are so small and so cramped, you CAN'T drive well enough to make it a nice experience and they just get soured completely by it. There's not enough trust in the world to convince a horse for the 12th time the trailer will somehow "get better" when it sucks every time for them.