Well, Stephenie said this about that in the Personal Correspondance #10 that she had with the Twilight Lexicon:
"What Jasper does effects not the thoughts, but the body. He doesn’t make you THINK you are calm, he actually puts your body into a calmed state. Or angry, or whatever. It’s physical rather than mental."
If you think about it you can kind of see that in Twilight when they are in the hotel room. Yeah, she feels calm but her thoughts are still troubled and it feels weird to her that her body feels one way and her mind another --or I guess that's just how I saw it.
@jessica-No I cud of sworn she actually got upset wen jasper was controllin her emotions at 1 point but she cudnt snap outa it. I think it was in New Moon.
@ashleigh- emotions r mental lol. Deyr not physical