Thats funky. I think I can explain it at least partially though. If I'm reading right, you helped both Duty and Freedom quite a lot, to the point of which both factions considered you _almost_ their friend. As a result your reputation with both factions was quite high, so when both sides started shooting at eachother with you in the immediate vicinity, they
both expected you to help them out, but you didn't. Because of that both sides now hate you. They trusted you, and you betrayed them as far as they see it. Their attitude is now "the enemy of my enemy". Congrats!

The relations really is very complex in TK and anything that does happen is based on your relationship with that faction or factions. There is some exceptions to this though such as random stalkers or factions members being red at you while others are green or yellow. That aspect is not based on your reputation, but the NPCs reputation. The lower the NPCs reputation, the more chance there is of him turning on you because hes considered somewhat of a rouge. Hope that helps explain the relations in TK

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