Whistles and yelling are strong stressors and only serve to work cattle up. Visually stock are sensitive to contrast and shadows . They don't want to go into an opening that appears as a dark hole. Handling areas need indirect lighting , not bright lights, shining into animals faces or casting deep shadows. Look at what your animals are afraid of and try to remove these stressors from the alleyways and chutes.
Details bother animals .
Do as Dr. Grandin does and walk through your system at animal level. Little things like a foam cup in the chute, a plastic bottle tied to a post and rattling around or the reflection off a car windshield sending bright light through the gap between fence boards can be the cause of balking. Solid sides work best for chutes eliminating any visual distractions. Researchers recommend walking through hog finishing pens 10 to 15 seconds per day so animals are use to people and not afraid of you. Walk quietly and enter from different directions each day.