Adobe CC is prompting me to upgrade Premiere to Version 7.1 but I haven't done it because their upgrades frighten me.
Then that is not the issue for you.
Does your file show as "Do not transcode"?
I am not CC. But as Jim points out, this is not a normal problem.
Operator error is always a possibility. Or oddities in workflow that none of us are focused on. Do you have any gaps in the audio in the PR timeline?
You might redo the process, and provide screenshots of the actual export.
The latest update for Encore CS6 is 6.0.2.004. I don't recall what it fixes.
