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I wonder if maybe the bird had worms, then when the treatment started the worms died, but there was already an infection and then just took off. Or the body would have to go through some sort of stress to weaken the immune system long enough to allow an infection to start and take off.

Hopefully Kathy will be able to be more help. I can't figure out which organ is which except for the intestine.What sort of plants do you have around your property? Going through my vet book there's only a few diseases that would affect the respiratory and GI tract. Few of them, if positive will...