Ok, I fixed my CS3. Heres what you do.
I downloaded some random mpeg file and imported it to my library.
The first option to make sure you set is to embed it into the
swf.
As you go through the options, set the audio to a seperate track. Not integrated.
After its done encoding. You should have two files in your library. The video and the audio. Drag the video out and it will ask you to make an X amount of frames. Go ahead and say yes.
As for the audio, just drag that out onto the stage on the same layer as the video is. Then test the movie and see if it works.
That worked for me. hopefully it will work for you...