ok i am not a very experienced user and i really am not good at trying to figure these things out lol but go through the steps
1) What video card do you have? Does it meet the req of hulu and flashplayer?
2) Are you using real flash player or gnash and other variants? Use the real adobe flash
3) You may have a codec screw up somewhere, make sure you have all the mp3 and mp4 codecs you think you would need, like gstreamer very bad, ugly, faac, faad, and etc. Sometimes the files can be in a container like .avi and will use mp4 video but mp3 sound.
4) Hulu desktop needs at least 2 GB of Ram http://www.hulu.com/labs/hulu-desktop
that might also be a reason why things are choppy
5) Ur internet connection? For smooth video performance without hassle a 2 Mbps Internet connection would be needed.
hope this helped at all