If I am reading correctly, you have two breeds of chicken, and have been setting eggs from both breeds under the same conditions and one breed you are getting good hatches with, the other you are having terrible problems hatching? And you also have had bacterial infections which appear to only have affected the Ameraucana birds?
I'm a duck person so don't know anything about chickens or chicken breeds, only anything I've read which was relevant to ducks also. But it seems to me there is some sort of health problem affecting only the Ameraucana chickens which is impacting the hatchability of the eggs.
The roosters from what I read, are unrelated, so it's unlikely to be rooster infertility or some other problem coincidentally affecting all roosters.
I'm not sure if your hens are all related? If so, possibly there is something genetic there? Or some health issue that they or their other had which has affected their ability to lay good hatching eggs?
The only other possibility would see to be something in the environment which has caused problems to all the chickens of that breed which have affected fertility. Not sure why only that breed would get a bacterial infection when the other breed did not, unless either the hens are related and have something genetic making them more susceptible, or the Ameraucana breed itself has a genetic susceptibility to the infection that they got..
Anyway, if you can rule out the incubation environment (because the other breed you have is hatching well) then it seems to me it must be something either genetic, either species level genetic weakness/susceptibility to certain bacterial infections etc, or inherited weakness - if all roosters, or all hens, are related to each other.
Or if your hens and /or roosters or their eggs, all came from the same place, something environmental there.
Have you done much research on that particular breed and any genetic tendencies it might have?
I mean all breeds of whatever animal, are usually created by someone intentionally breeding an animal to have more of a certain characteristic, and often as a result, they also unintentionally breed mutations into the animal which result in a higher incidence of particular health issues. So is it possible that Ameraucana chickens have inadvertently had bred into them, some susceptibility - either to certain bacteria, or to infection with certain bacteria resulting in long term impact on fertility, or just a genetic tendancy towards infertility...
I'm just pondering possible reasons...as above, I don't have any experience with chickens, much less insight into genetic considerations for different breeds. But maybe there is an Ameraucana expert here somewhere who does have some understanding of anything genetic in the breed that might be a factor here?