Did you or your trainer check his back for soreness? There is a correlation between the neck and the last vertebrae in the spine.
He may be stretching his neck to say he needs to release or fix his back.
Another possibility is irritation in his larynx. He could have eaten something that caused his throat to be inflamed. Horses will stretch to avoid a closed feeling in his throat. Did you give him new hay? Different turnout? It can also be molds and late pollen in the cup hanging season.
Hope that helps.