I don't think that you can fix it. I just bought an apple tv & installed boxee. I get the choppy frame rate. From all that I've read, it is a limitation of the hardware. IIRC, the apple tv comes with 256 megs of Ram & the apple tv software, plus the Hulu video stream plus the Boxee software runs at something like 105% of the available Ram, so it will always be choppy for playback.
Love my apple tv & am glad I got it, but I do wish hulu would run on it.