You know, with the first chicken (the one who died last year) I don't think I'll ever know what it was. And we didn't treat her for any parasites. We'd given her antibiotics to no avail ... and chicken x-rays, blood tests, nebulizers, oxygen, etc. That poor chicken.
When the next chicken started making the sound we went to see the breeder. First we tried the ivermeck for general parasites. When the problem persisted, she suggested that we treat for gape worm. After a treatment for gape worm, the problem went away.
It came back again, months later in another chicken. It was co-incident with runny poop and broodiness too. We went back to get the gape worm treatment it went away.
So, now whenever we hear a funny honking or squawking and see them craning a neck, we head back for the treatment.
I have not done any tests to prove that this is what it was. But the treatment seems to be working. Our breeder advised us to treat for parasites every 90 days (topical as well as internal).