I would bet the queen never left the hive. It is quite hard to get the queen to leave the brood. If that were the case, one could simply dump menthol into the cavity to get the bees & queen of a swarm out of a wall or tree. I wish it were that easy :) Although I use the paper towel method, I have noticed that different hives can react quite differently to menthol. All my hives received the exact treatment and this was the worse reaction hive of mine this year.
click image for larger view
Within 2 days they where back in the hive. I had one other that had a handsize cluster hanging, but most hives, although very active trying to ventilate at the entrance, did not cluster on the outside.
Hope all is well with your hive by now.