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I suspect a lack of careful breeding. Overmedicating - possibly.
A lot of people who are into this commercial medicate everything. They feed antibiotics in the feed, antibiotics in the water, etc to keep any bug from having a chance to live. There's also a lot of literature that pushes for using antibiotics to increase growth rates and thriftiness - but really that's designed for huge industrial farms.
I'm just catching up because for some reason my 'subscribe' to this post was bumped off and missed everything. But because of the two working vents, I'm glad you're not going through with the surgery. I suspected it would have just killed her, and that's why I was hoping yo uwould mention it before taking her to a vet. The vets I know wouldn't be likely to do it and would advise you of the same about the multiple organs.
This should be interesting. I'm glad that she's doing well. She might break your heart in the end, but at least she's got a shot at life.
As for the hatching, and mushy bellies, here's a good site: some of this could be hatching conditions (though I doubt all of it is - certainly not the malformations, but possibly the mushy bellies). It never hurts to have a good site like this for anyone hatching out babies:
http://msucares.com/poultry/reproductions/trouble.html#RN
In this case, I suspect heredity.
Funny - I've seen those hatching eggs on
ebay and wondered..