the only time they slept together prior to being in a relationship was in ch.1, when kuon went over to the shirahane's. that aside, the cold/distant mood around their interactions is all explained by kuon's image of Nanao being distorted by the rumors/nanao pining after him despite being aware that he's disliked. maybe you did misunderstand something?
Okay, now I feel completely stupid. I've read the first chapter late last night half asleep and the rest of the story this morning, so I had completely forgotten what happened there and only now after you pointed that stuff out and I reread the first chapter I realized it....... really ought to fix my habit of reading manga until way way way too late
So, is their previous relationship explained in one of the later stories? I mean they seem to have slept together before this story or am i misunderstanding something?