I just created a new swf file embedded in an html file as a first test, and the sound starts drifting after a few seconds. The farther into the file you go, the farther off it gets. I had it create an mp3 file at the same time. Is that the problem? I'll try creating them separately, but part of why I bought the encoder was so I could do both at the same time.
By the way, the final video product was similar in size and quality to Sorenson Squeeze 4.1, with the exception of the unbundled audio/video.