First things first: apparently, according to Favreau, the movie ended up "darker" than could accommodate Munn's first appearance, implying that it was somewhat comedic. Second, what director ever likes anyone so much he calls them back for a second, all-new role? Since I feel reasonably confident Olivia Munn is not the second coming of Meryl Streep, I think we can all safely assume that Jon Favreau is having weird sex with Olivia Munn, and wanted round 2.
Third and most importantly, who the hell was she playing, and who the hell is she playing now? I did get several emails with zero proof saying she was going to be play the Scarlet Witch; while Munn does look like Wanda Maximoff from The Ultimates and the Scarlet Witch is a minor enough character to be a cameo without fucking up future Marvel plans, it just doesn't seem right to me. io9 suggests she might be playing The Wasp, Janet Van Dyne, but since I'm pretty sure that character will be an important part of the Avengers movie (important meaning "token superheroine") I doubt Favreau would have access to that character, or that Marvel would approve such a cameo. My money is that she played or will be playing SHIELD agent Maria Hill, since Sam Jackson's Nick Fury and SHIELD play a larger role in Iron Man 2, and Hill is a brunette like Munn. And I don't think we can count out "random Tony Stark skank" for either appearance.
I'm guessing she played "random skank" in the first scene, it ended up a little too silly for the complete movie, and now she's going to show up in SHIELD as Maria Hill and in a SHIELD uniform. Who wants to bet against me?