[Brent Ross]

I have been having the same problem an have tried many techniques to solve the problem. And through a stroke of luck, I seem to have found a method that works pretty well. What I did was jump into the Premiere file and select one of the sequences that didn’t have audio in Encore and set up to render out an mp3 of just the audio. But before actually starting the render que in Media Encoder I hopped back into Encore and the audio was working. After trying everything I could think of this seemed to do the trick. I think it may have caused the Adobe suite to kind of kick into gear and sense the files properly when I went to export the audio.

Hope this helps