If your eggs are being fertilized then it's likely a different issue than the rooster. The odds that only the eggs you kept to incubate were unfertilized doesn't really make sense. You might have a problem in the storage (if you're storing at "room" temperature that can be too warm) most recommend somewhere around 50-60°F and that is fairly cold and isn't room temperature for most people. I don't have any other ideas if your eggs are being fertilized, your incubator worked fine on eggs shipped to you, but not well on your own collected eggs, then to me it's the storage/handling of the eggs before incubation.Yes, I have cracked eggs and they are fertilized. We give crushed oyster shells.
I don't hold eggs for incubation past 10 days and do not turn them. I collect them a few days in row, inspect them for shape and cleanness. They are stored in the same room where the incubator is.