I created a series of three similar projects. Each has a three second audio clip in scene one and a long audio clip that plays through the rest of the presentation. In Hype 2 I had no problem outputting the video with audio.
In Hype 3 I swapped out a logo in each and reoutput them. With the first attempt only the intro clip showed up in the video. With the second attempt, not audio was output at all.
I have no idea how to fix this. Because of the way the upgrade worked if I tried to use my copy of Hype 2, it automatically launched Hype 3.