I'm also another smoker who has never experienced anything like that directly relating to my smoking...but who knows, it could be the way your body is reacting to smoking? But it really does sound like breakthrough bleeding to me, which can definitely be gunky/sludge/snot like sometimes (i notice breakthrough bleeding to be particularly snot like if i was aroused at any point in the day too) and the brownness of it all just sounds like old (oxidized) blood. The fact that you are near the end of your HBC 3 weeks and the anti-malaria drugs could also be playing a much bigger role then you are giving them credit for. i'm not a doctor by any means, but i do think the brown discharge has more to do with either of those, then it does to social smoking.