Mulder's neurological condition in "Biogenesis" and "The Sixth Extinction"

What was the cause of Mulder's neurological condition in "Biogenesis", "The Sixth Extinction", and "The Sixth Extinction Part II: Amor Fati"?

Was it his prior exposure to the black oil in "Tunguska" and "Terma"? He was given the weak vaccine just prior to exposure at the end of "Tunguska", which seemed to effectively prevent his infection. I recall Michael Kritschgau explaining a connection to Mulder's experience at Tunguska at some point in one of the three aforementioned episodes, but how does this square up with the vaccination?