I had a similar situation last year when my queen was laying in every cell, but the pattern was very spotty by the time there was capped brood. In my case, it turned out to be the early stages of European Foulbrood. 

Apparently, the workers (from a hygienic queen) were eliminating all the eggs or young larvae that seemed ‘wrong’ to them. So I didn’t see sick brood until the hive was pretty overwhelmed by the infection. Then when I finally found a suspicious larva to test, I got a positive EFB test. 

I have also heard of hygienic-bred queens producing workers that “over-express” the hygienic quality and eliminate almost all eggs. 

Are NONE of the eggs hatching? Or do you have a spotty capped brood pattern?

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