I had the same problem with a swarm that I hived. There wasn't a queen for a while until the queen cells hatched. I had timed about when the population would jump, and put a second deep on well in advance. They didn't draw it out, and when the capped brood emerged, the queen took them and swarmed. I guess they felt too crowded in the bottom box, even with the top box that they didn't draw out. Now I'm in the same situation again with waiting for the new queen to emerge, mate and start laying. Hopefully, in the meantime, they will draw out the top box this time!