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I had a capped supercedure cell in one of my hives (which had gone queenless) a couple of weeks ago. Checked out the hive yesterday and found a frame or two of eggs. About 20% of the cells had 2 eggs per cell. I assume the queen just hasn't hit her groove yet? How long before she settles in and leaves only one egg in each cell?
 

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Give her a couple weeks. Watch the eggs that have been laid to make sure she's laying fertilized eggs and she's not a laying worker or poorly mated.
 

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Multiple eggs in a cell shouldn't happen with a queenright hive. In fact, it's a pretty good sign that your workers are laying--not a good thing. You could watch for a couple weeks, but your hive's population has already dipped if it's replaced its own queen, and it'll dip a lot lower if this is a laying worker problem. That low population is going to make your hive vulnerable to nasty problems like wax moths and robbing and a host of other things...anyway, I'd recommend dealing with the problem sooner rather than later. Here's what Michael Bush has to say on the topic:
http://www.bushfarms.com/beeslayingworkers.htm

Good luck!
3pianists
 

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If 20% have 2 eggs - then 80% of the cells have a single egg in the bottom of the cell (if I'm reading your report correctly). If so, then my guess is that it's probably not laying workers. In the laying worker colonies I've had experience with, the majority of the cells have multiple eggs and some on the sides of the cell wall. If you only saw eggs in your last inspection, and no larvae yet, then she just started laying within a few days. I would give it another week and check again before making any decisions either way.
 

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Make sure she has enough open cells, A new queen might also lay multiple eggs if she doesn't have enough room to lay like crazy.
 

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"Multiple eggs in a cell shouldn't happen with a queenright hive. In fact, it's a pretty good sign that your workers are laying--not a good thing. "
I have a hive that has shown two-egg-cells for a couple months. I initially suspected laying workers, but then all the emerging bees were female worker bees. Then I discovered then answer to the riddle. The other day, during a hive inspection, I was examining a frame of brood. I turned it over, and there on the same frame were two queens! They seemed to be getting along just fine. Not sure how that happened. Thoughts anyone?
 

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It is actually not that uncommon. You will eventually have only one.

As far as new queens laying multiple eggs in cells. I find that a lot in my mating nucs. It has always stopped within a few days of her starting to lay.
 
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