I assume you're talking about the event in which Rin confronts you about the photo exchange. Played it just now and it's fine, game recognized my good homie flag no issues. If it wasn't a mistake on your part, all I can think of is that for some reason something broke in the update with regards of giving the proper badhomie/goodhomie flag early on, but I'd have to replay that segment.
There's not much difference.
However, since I had to replay the event for this, let me just say this is one of the hottest conversations in the game, courtesy of green path:
When, Selebus, when?