Even if they are getting a bad headache everyday that would be super bizarre. How bad was your office environment if almost everyone is getting headaches every day?
I suspect the "every day" part was not accurate and it was just headaches they were getting not migraines. But a migraine meant they were sent home (no pay) a headache wouldn't allow that although I do know they truly believed they were migraines.
I don't care much for ventilation systems in general ... never really works all that well, and are vastly inferior to just opening a window. Some are noisy, too.