Is it just random patches, or near roof ventilation? If random I'd third the fungus thing. Is the roof ventilated? Attic conversions without adequate venting can promote growth of junk. Do you see signs of moss?
If the dark spots are around vents it could be smoke damage. Usually also shows up around the soffit vents.
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There are a vast number of people who are uninformed and heavily propagandized, but fundamentally decent. The propaganda that inundates them is effective when unchallenged, but much of it goes only skin deep. If they can be brought to raise questions and apply their decent instincts and basic intelligence, many people quickly escape the confines of the doctrinal system and are willing to do something to help others who are really suffering and oppressed." -Manufacturing Consent: Noam Chomsky and the Media, p. 195
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