It has been my observation, as well, that as the nectar flow slows down, the bees leave a lot of nectar uncapped.  Why?  Don't know.  My guess is they think they're going to eat it in the near future.  Why cap it?
 
In a normal year, our flow ends around mid-July.  This year, it's been extended due to a late spring and timely rains.  I'm reminded the only place I find "normal" is on the washing machine in the basement.
 
My old solution was to remove the supers (which are free of brood as I slide in an excluder in mid-June) and set them out to be robbed out, cleaned up, then treated for storage.  I used to overwinter in double brood boxes.
 
Now I break down the hive after the honey harvest, make splits and generally configure my splits into brood/med super or a "story and a half" and prepare for fall treatments, feed, etc.  If I've caught some late swarms and have them in singles, they get one of those incompletely capped supers.
 
Yes, you'll get your super "broody," and the wax will darken, but it also toughens it up for next year's extraction.
 
Grant
Jackson, MO

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