I have set up a train ramp with 2 bounce pads and a straight rail at the end for landing. When I run the train in manual mode it lands properly but when I run it in automatic with the same run-up distance, the ramp and bounce pads work fine but the trains all just explode on landing at the rails. I tried with and without a destination station for the train to reach at the other end, and I tried with the ramp on both modes and it still hasn't worked. Could you help me understand why?

Do you have a picture of the setup and the train's schedule? It's important that the train has a usable path to it's next destination when it lands. If it can't find one, it'll land and freeze and the following carriages will crash into it and explode. If you drive in manual mode that won't happen because it doesn't have to look for a path if you're driving