Paralysis --> clean necropsy in affected (vaccinated) bird --> now another paralyzed bird?!!?

Unless you sent the bird out for testing, I would not rule out Marek's or another disease, especially with multiple birds dying across different flocks.

If you look at this page (http://marphavet.com/en/news/Disease-Treatment/Marek-s-Disease-MD-in-chickens-79/), you'll see that there are different forms of Marek's. Some forms are more visually apparent than others. I often see people talk about tumors from Marek's, but that may only show up in the visceral form. You may be dealing with the neural form which causes nerve enlargement that you likely wouldn't notice if you aren't trained to look for it. I've done many gross necropsies and I wouldn't count on my ability to detect it.
 
There’s been an emerging disease called enterococcus spondylitis, or a form of kinky back, it’s a normal part of their gut flora but for unknown reasons it’s been seen to invade the spine and cause paralysis or neurological disorders through inflamation pinching off the nerve. I don’t know if that’s the cause but maybe look into that.
Can you post any links to information about that?
 
The chicken was pretty young for Mareks, so it may be that signs were so small or microsopic to see during a home necropsy. In slightly older birds we may be able to see small tumors on the internal organs. Mareks also lowers the white blood cell count, so chicks may have decreased immunity and a hard time fighting off common infectious diseases.
 

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