My thunderbolt does the same thing. the video converter i have on my mac i had to up the video and audio bit rates to maximum but i still get some picture chopp and some audio distortion/blippy only when people are speaking on the movie no other parts of the movies are affected which is weird. Also the audio distortion only occurs with headphones i tested a youtube video and no audio distortion. So my guess it is the tbolts video player or the way it processes video. or it could be my video converter which it isnt because i test the movies after i convert them and they play perfect on my computer except for a very slight audio distortion at random. But all distortions and picture jumpyness are magnified by 2-3 times on my thunderbolt. Which leads me to believe that the thunderbolts graphics/video/audio card may not be up to the task of playing mp4 movies even with the newest codec .264.
But i am pondering the idea of returning the tbolt and waiting for the Droid Bionic which has Nvida graphics processor and larger battery which may yield better battery life.