Spite.
Iron Man's armor and arc reactor had advanced greatly by the time the Avengers came around. Stane fought an Iron Man with like 5% power while the one Thor fought had 400% power on top of what I previously said.
And this is just a plain bad match up. Iron Man used his mobility and maneuverability a lot to hang with Thor. When he tried to match up strength wise, he was getting dominated. Stane's all brute force, he's like a cheaply made Hulk.