Seems like your setup is corrupted. Please pull a fresh copy of HB and try the fix again.
EDIT:
For those following this certain issue we resolved this over PM with the new HB he pulled and the fix he was able to successfully run the Dungeon he was having issues with.
With thanks from ZoneHunter this fixed it for me so if anyone else are having problem with the bots not completing the dungeon and skipping bosses try do a fresh copy!