One thing I've noticed with non-organic treatments is that once you give one treatment it becomes a never ending cycle. You wipe out the immune system and begin having to treat everything. I don't even use the medicated feed for my chicks for this reason, although I'm careful to raise them on as dry of ground as possible, even raising a roof over the pen or putting them in abarnstall when I lived in wet climates.
This is something I've noticed not only with chickens but with my garden and with puppies, calves, horses and even the people I treat. ( I'm a physician) I'm a huge proponent of organic methods, probiotics (kefir, kombucha, ACV and plain old healthy manure!) and making sure the good bugs are able to balance out the bad bugs. For example, if you have a bout of aphids in the garden and kill them with chemicals, you will poison the good bugs and be stuck using poisons the rest of the season to kill not only aphids but other pests.
I've seen how amazingly complex the organic cycle can become. This summer, our neighbor, who sprays all the time, for everything, came over to our house complaining of a tick infestation. I noted that I'd had a couple of ticks on the dogs but nothing bad. He said he'd pick off almost a hundred on his one dog, even after having his yard professionally sprayed weekly for a month. My theory is that he's been spraying so long that he has no natural predators such as birds and praying mantis visiting his garden. I had huge amounts of mantis this summer and desert cardinals everywhere.
I hope you give things another try.
Organic cycles are simply so complex that it's nearly impossible to track the cause and effect. However, I would say in this case, starting fresh, with a different source of birds, new dirt, and a new philosophy would be a good place to start.
I give plain old, non-medicated chick starter, along with ACV and some kefir. I start on some sprouts and greens, adding some tiny grit right away. My chicks are healthy and strong.
For what it's worth, I don't vaccinate for much, either, only Marek's, because it's becoming so virulent. Anytime you vaccinate, you put a severe stress on the animal's immune system while it's responding to the vaccine. By vaccinating for multiple diseases all at one time, you are allowing other opportunistic diseases to take their toll, just while the stress of shipping, hatching and being a tiny baby chick are also happening. I think it's simply too much. I would save vaccines for times when you have a known outbreak or known problem disease in the area, such as a fowl pox outbreak.