I tried to lower the resolution and it didn't really do anything. The FPS (ctrl alt f) in game is fine (well actually it drops from the normal 160 to 30ish). I have all my SC2 settings on low.
I loosely followed the tips in day[9]'s blog from long ago. I've noticed this choppiness ever since I first began to stream, but I've just been managing with it otherwise. I'd like to stream every time I play, but I don't because I don't wanna be hindered all the time by this.
edit- I think I figured it out, there is a setting to control game FPS and that seemed to help (doubled it to like 60-70) not as bad, still some frame loss though.