Pepper was given the drugs, or whatever it was to make her heal, and heat up. Did that ever get removed from her system, or is she still like that? We see no examples of it after that movie, but I don't recall a fix being given.
It's stated In Iron Man 3 that Tony fixes Pepper to remove or at least stabilize (per wikipedia) the Extremis changes.
As promised, I got Pepper sorted out. It took some tinkering.
after Pepper was concerned...
Pepper: Am I gonna be okay?
Tony: No. You're in a relationship with me. Everything will never be okay. But I think I can figure this out, yeah. I almost had this 20 years ago when I was drunk. I think I can get you better. That's what I do. I fix stuff.
Yes, he cured her before she burned out.