You must have done something wrong; I just redownloaded it; replaced the files, played the story and it worked fine. I can't see how it couldn't possibly work; since I even added a line in the script file to directly teleport the player to the right place when the map starts
EDIT: I can 100% confirm that v1.03 fixed this issue. If you downloaded it, you will need to reload the entire custom story/the hallsofblood2.map to see any effects (providing you deleted the "An Unexpected Arrival" folder, and replaced it.