In the first episode it is indicated that Agents of S.H.I.E.L.D. happens after The Avengers, but the first episode also has Extremis in it. So is it a pre Iron Man 3 version of Extremis or post? I mean if it's post then why didn't they already have the Extremis solution (which is used on Pepper Potts)? So why to waste time in making Extremis again. Or is it a pre version?
Pulling from the The Comic Board Forum (and from IM3), we know that:
These are the time based events. We do know Stark helped Potts make it through the Extremis transition. What I believe is not spelled out is we do not know if the "bad guys" know what that "cure" (or help) was which Stark provided to Potts. They (the bad guys) are still working with Extremis trying to fix these problems. The SHIELD team is trying to counteract the effects of the Centipede (people blowing up). They aren't necessarily trying to cure Extremis in these people.
EDIT: As seen in my revision of the chronology thread, I have made some updates to this thread here which makes more sense, but does not invalidate what I'm saying.