When the bees leave the cone, they go to the field. Upon their return home, they cannot get in, so they go in the trap box. When the queen leaves, she also goes to the "field", or the woods. To a tree as a swarm, or whatever. She never returns, therefore she doesn't take up in the trap box. She absconds with the few bees left, as she doesn't know all the others are just outside. All she knows is she has no food and few bees, so she's getting out of dodge fast.
PS. Pics and follow up posts are highly sought after here. We expect you to keep us up to date on the trapouts.