I'm personally of the opinion that they've been going at it since before the series opener and that the sir bit was Ianto trying to cover it up. Except for in the harassment line, there I think he was teasing Jack back.

I was kinda wondering if the hand thing during the kiss because the guy playing Ianto was nervous and John was trying to help him just get through it. One never knows, and no one seems to be asking John about it on the billion talk shows he's been on recently. *shakes head* Silly talk show people.