I'm mainly just subscribing here because I don't have any bright ideas.
But when you say a vet found nothing wrong, have any vets actually witnessed this behaviour in the process? If not then you might want to think about trailering your horse to the vet clinic, so that a vet, or even multiple vets can see him in the process of having these episodes.
Does he scramble around corners, or stand with his legs widely spaced apart or anything of the sort that you can think of?
My gelding had always been trucked before I got him and I had to teach him to float, even to back out of the float (he would stand patiently and wait for imaginary front doors to open). He scrambles around corners if the driver goes too fast around the corners, he has ripped the front of my partition out leaving it swinging by the bum bars, and also managed to roll the mats up underneath his front legs, but he has never actually gone down in the trailer or appeared to be seizing, I think this definitely warrants a second opinion from another vet.
R.I.P ~ Bubbles - 25yo tb mare - 13.04.2011 ~ 8:30am ~ passed away naturally and peacefully in my arms