OP mentioned having vaccinated AND unvaccinated birds. Depending what they were vaccinated for could be a cause, not sure though. Probable cause sounds like Marek's disease as
@Wyorp Rock mentioned.
Untreated well water: Our well water is untreated and currently have iron water and we had hard sulfer water in Georgia and have had no issues with chickens.
However, if the well is near a septic tank/drain field, or agricultural chemicals leached into the water table, there could be problems not only with the chickens, but with people as well.