The Officer Barbrady is incorrect.
This is my 3rd Iron Banner, and I can say confidently (because I watch it happen every single match) that if you wear a Faction Mark/Bond/Cloak, that you will gain Faction Rep and Iron Banner rep with a win. If you lose, you will still gain a small bit of Faction Rep and receive an Iron Medallion for the Iron Banner.
So with a win, you will gain Faction as well as Iron Banner reputation.
With a loss, you will gain a smaller amount of Faction rep, and an Iron Banner medallion.
In the case of Bounties, this is the same as Eris. Regardless of the Faction item you are wearing, you will still receive Iron Banner rep. Iron Banner bounties only award Iron Banner rep, not Faction Rep.
Regular Crucible bounties (which can also be completed while fighting in the Iron Banner) will only award you Faction rep, never will they award Iron Banner rep.
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This is correct.
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Thank you for a detailed answer. I didn't know you could wear your class item when turning in Eris bounties; I've been taking mine off...I didn't mean to imply that Crucible bounties award Iron Banner rep. Good luck in your fight.
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Glad I could help. :)