So, I looked at the code, and the only conclusion I've been able to come to is that you've already defeated the Lich King -- and therefore have already defeated the Witch Queen too. I changed the code in the next version so that Raphaelle doesn't have the "How do I unlock the Crypt" option if that's true. But when you defeat the Lich King, the catacombs collapse and therefore don't appear as an option. And that is the *only* situation in which the Catacombs do not appear.
if not lich_king_defeated:
textbutton "Catacombs" action [SetVariable ("venue", "Dungeon"),Jump("Adventure")]