Usually putting a queen excluder over two deeps encourages bees to pack honey into the second box late in the season. Of course, I don't do this, so I end up with hives like yours with most of the honey in the supers. I settled on leaving them in three stories: two deeps and a medium. I don't consider brood or pollen in the supers to be a problem though, so I guess this isn't much help. It's a balancing act, I suppose. If you don't put as many supers on in late summer, you would force the bees to pack it in the brood box, but I usually put on as many as I have, ever the optimist. (I am running about 12 hives, also. I have enough supers to give every hive 4 or 5 mediums over the two deeps, no excluders)

hope this helps, or at least lets you know you are not alone in this problem.

Pete

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