Sounds like they are hurting a little bit for room. With 90% of the bottom and middle box in use, not much room for the queen to lay, and bees don't equat undrawn comb as usable space. Maybe you can checkerboard some of the foundation from the top box down into the second box and get them growing again. Frequently, when adding foundation, if there isn't a strong flow, the bees just seem to stall. Thats when checkerboarding, baiting them up with some brood, comes in handy.
It's also difficult to tell sometimes that they have swarmed. The queen lays the hive up full, stops laying, gets in flying trim and leaves with the swarm. All the emerging brood quickly repopulates the hive. It's the gap in brood rearing that indicates something has changed. When this happens, they frequently set themselves up to cast another swarm fairly quickly. With no brood to feed, all the nectar goes into storage, and a honeybound condition is created. Guess what they do when honeybound?