The Encoded Files have after Encoding no Audio Tracks. As i had never similar problems before, i think its a Bug! Where can inform the Adobe Team?
You can certainly file a bug report here: Feature Request/Bug Report Form but there is no guarantee you will get a response. These forums are your best bet to get help on the issue and the team does watch the forums from time to time. Also, as it is a user to user forum, the other users here are pretty good at helping each other out.
Can you give us some more details about what source you are exporting and what preset you are using?