okay yankee, my guess is that a flow started and they were bringing it in before you realized it and before supers went on, so they started packing it away in the 2nd deep. so the bees are a bit organized, like with supers, they don't work them all, they work the box their in, before moving to the next one.......if this makes sense? if you have drawn comb in the supers above, the excluder is not the issue.
what's in the bottom deeps?