I have been having this same problem this year also. First round of acceptance was awfull. Did everything just like last year. Make up mating nucs on Sunday and Monday and put queen cells in Monday afternoon. Cells normally hatch Tuesday around noon. Cells not used in nucs were left in incubator to sell as virgins.
When I went back to cage queens only got around 30 % takes. Probably 50% had young virgins running around. You could tell the queens emerged from the cells but they killed them and raised their own emergency queen.
Thinking back I remember that the virgins were emerging from the cells in the incubator later than normal. I have changed to placing the cell in the nuc to Tuesday morning. It may be that the longer it takes for the queen to emerge it gives the nuc more of a chance to start emergency cells of their own and then kill the queen when she emerges.