First, on the Character/Profile tab, have you added the new faction? You won't be able to record fame for something until there's a place in HL to store it.
The value you put in "Fame and reputation awarded" will be placed in the faction of the currently slotted champion boon.
The value you put in "Reputation Awarded" will be placed in the faction you set for "Faction for reputation awarded" - if the issue is that there's only one faction to select from in "Faction for reputation awarded", then add more factions on the Character/Profile tab.
So, for example, on one of my own characters, for Yesteryear's Truth, I entered "Wayfinders" in "Faction for reputation awarded", 1 in "XP amount", 2 in "Fame and reputation awarded", 588 in "Credits", and 1 in "Reputation awarded" (because of the scenario's faction tag)
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