Steve Rose 
>Could the bees be sensing a problem with the pupae, such as AFB, then removing the worst and leaving others open so they can be monitored?<
Maybe. Perhaps either a parasite, disease or chemical irritant is causing the bees to uncap or cap in strange way.  More likely that than a genetic problem, but who knows?

Randy Oliver:
>Is there any chance that that hive had been exposed to some pesticide?< 
Extremely unlikely, though we can't rule out chemical exposure of some kind interfering with the bees' signals to cap or uncap cells.  Only affecting this one colony, though.

If we can't diagnose, I may ask the beekeeper to experiment by taking a frame of larva from that colony and placing it in a normal colony to observe how it is capped.  Similarly, move a frame of larva from a normal colony into the affected one.
John



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