We just found three more Queen cells. Two in the lower brood chamber and one in the upper. We found the Queen and it appears to be the same one. We also found lots of brood. The three cells were opened and I assume she has killed them. There's plenty of room in the upper chamber. Not sure why we're finding Queen cells. Oh, and I got my first sting! Bummer...
It might be because they were already in swarm mode when they were supered. Bees in swarm mode will usually not build new comb until they have completed the swarm cycle. You can sit there for weeks wondering why they won't draw comb when suddenly they swarm. The the bees that are left move up and start building comb.