If you load the map, then fiddle with the siege tower when it's no longer in final position, you will screw things up. Happened to me several times. Just delete everything belfry-related, reload the map and redo everything in ONE GO. Don't save in between, only when you're finished. Then exit the map, reload, and all should be fine. If you later have to adjust the siege tower parts, make sure to push it to the wall completely first.
Same reason why ladders sometimes get wonky, btw. Oh, it's possible to push the belfry all alone, btw.