My current Faction Leader lost an eagle early in the game and got the trait 'Disgraced'. He has now taken the town that the Eagle was being held in but did not get the expected 'Reclaimed Eagle' trait. I found this code in export_descr_character_traits.txt:
Code:
;------------------------------------------
Trait LostEagle
    Characters family
    ExcludeCultures barbarian, nomad, greek, eastern, egyptian, carthaginian

    Level Disgraced
        Description Disgraced_desc
        EffectsDescription Disgraced_effects_desc
        Threshold  1 

        Effect Influence -4 
        Effect TroopMorale -2  

    Level Utterly_Disgraced
        Description Utterly_Disgraced_desc
        EffectsDescription Utterly_Disgraced_effects_desc
        Epithet Utterly_Disgraced_epithet_desc
        Threshold  2 

        Effect Influence -8 
        Effect TroopMorale -4  

;Mod149 - 11/02 : added -2 troop morale per level, removed antitrait
;------------------------------------------
Trait RegainedEagle
    Characters family
    ExcludeCultures barbarian, nomad, greek, eastern, egyptian, carthaginian

    Level Partly_Redeemed
        Description Partly_Redeemed_desc
        EffectsDescription Partly_Redeemed_effects_desc
        Threshold  1 

        Effect Influence  2 
        Effect TroopMorale  1  

    Level Mostly_Redeemed
        Description Mostly_Redeemed_desc
        EffectsDescription Mostly_Redeemed_effects_desc
        Threshold  2 

        Effect Influence  4 
        Effect TroopMorale  2  

;Mod148 - 11/02 : removed antitrait, added 1 troop morale per level
So it appears to be in the mod. Could the removal of the anti-trait line (from unmodded version), or the fact the Eagle was held in a town not in an upgradable city, have resulted in not being awarded the 'Reclaimed Eagle' trait?