Slant load trailers do seem to be easier on the horse. You could try giving something to help her overall discomfort. One of my old mares seems to have more trouble now in the trailer, so when I know she is going to travel, I give her Easywillow by Finishline. It seems to work great for general discomfort. You cannot compete on it under USEF rules though, even though the Finishline rep at Western States Horse Expo was telling people it wouldn’t test.
Other than that, your vet and chiro are good sources for eliminating her discomfort. It could be just a learned response now though.
Arabian Sport Horses introducing kids to dressage in the Sierra Foothills.