I guess I misunderstood. Let me see if I get it right now - please correct me again if I'm wrong.
- there's brood in the first box
- honey filled in the second box
- then honey excluder
- no work being done in 3rd and 4th boxes (and maybe 5th box?)
I'm trying to get a good picture of this. First off, I know my bees don't like going past the excluder. If they're trapped up there when I put it on, they'll go down to the brood area, but they don't like going up past it. So if I've trapped a couple thousand bees up there, the next time I look, I might see just hundred or so.
Next, if they swarmed, when did the new queen get active? And this all started you say about 5 weeks ago? So given the fact that in the first hive the queen had to hatch, then do a virgin flight before laying, the brood in there may only be a couple weeks old. Where as, the other hive (the swarm?) had an active queen, and her first laying has hatched now. Plus she's gotten to lay more. Also, in the first hive (in this 5 weeks time) some of the bees have gone from being house bees to foragers. So you won't have that many house bees right now to do any wax building with no new hatching bees.
You said the top brood box is full of honey? And so the queen is only able to lay in the lower brood box? The hive doesn't sound nearly strong enough - even IF any of the first laid eggs have hatched - to be able to do much work. Is it possible the bees just decided to fill the empty brood cells with honey because it was easy? So they wouldn't have to pass the excluder?
And what kind of hive is this? Is it a langstroth, or something else? How come you only have 8 frames in each boxes? Is this just in the honey supers?
I hope I understood better now, and didn't end up confusing you with this post.