Michelle, You’re leaving the eggs on the counter!
Doesn’t matter if you’re collecting them twice a day, if they’re on the counter after there’ve been fertilized by a rooster, the embryo is still developing!
With a fertilized egg, you must bring them in and put them in the fridge to stop the process! Depending on the stage of development, you may still have a problem, but if you want any chance at all at having edible eggs, don’t place them in the counter, place them in the fridge! It’s about the temperature! Must stop development.
The sure fire method is to quarantine the rooster away from layers that you desire to consume their eggs. He can have his fun with the other girls, but not with the eggs you put on the table.