Stark is working on a way to remote control the suit
He's also having nightmares about the battle in New York.
He was nearly killed a few times in "The Avengers"
-Thrown out of a window
-Going into space on low power
-Nearly chopped up by the helicarriers turbine blades
-He was so sure that he wouldn't make it back from delivering the nuke he tried to call Pepper.
It's possible that Stark synched his brain waves to the new armor.
When he has nightmares his subconscious activates the armor. Stark's priority to "Protect" leaks into the armor
The armor follows by "Protecting"