Tony wasn't particularly comfortable around Bucky not only for the elephant in the room, but because he had no idea what time period he was from. Tony was far enough away from the "incident" to at least see things logically. He no longer blamed Bucky for killing his parents; he understood he was brainwashed. Understanding didn't make looking at him easier, but it did deflate Tony's anger. Bucky was a victim much like Howard and Maria were victims. In the end, Steve's secret and subsequent abandonment bothered Tony more than Bucky's act. However, he tried to kill the man - an innocent one, more or less. He had been in a rage so it was good Cap stopped him, but...
There was a lot of history between Bucky and Tony to say the least. It was ironic, given he barely knew the man. However, they were both in a new place starting over and he was a guest in his home.
"Barnes," he said with a curt nod. "Thank you for coming."