How many eggs are you hatching, what percent crossbeam are you getting? A new rooster is probably the best route to go.
Do you know who's eggs you are hatching, or do you just hatch what you have at hand. I think a new rooster, and most of this problem would go away, but even with a new rooster, I think a little more careful who's egg you are hatching, to see if you can figure out which hen needs to be culled.
However, I bought a couple of chicks, last summer, and I looked at them carefully. And 6 weeks later, I thought there was a stick in her mouth. It can take several weeks for it to be easily evident.
Mrs K