Two of my three characters reset affiliation for this rally but third didnt so I had to delete and start over to not miss out. Currently at lvl 6 and soooo tired of doing the campaign for like the 7th or 8th time. Two Red bulls cant keep me awake for it.(that is not a joke)
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I have also just run into this problem. Just swapped over to third character (titan) for faction rally. Was going to chose FWC for this character but game had him locked into Dead Orbit, which is the faction he was on last time.
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Your third had affiliated before? Are you saying this time around with the faction rally your third character could not assign himself/herself to a faction?