"There were a lot of WTF moments in this movie. For instance, Tony was willing to face a terrorist strong-hold without armor (using make-shift weapons from Home Depot), and we later find out that he has 41 suits ready to go at a moment's notice."
I think this was explained in the movie. It took awhile for Jarvis to get fully operational again, and for the construction crews to clear enough wreckage to uncover the opening to the Iron Vault.
BTW I just remembered that this movie name-dropped AIM and Roxxon, which was awesome!