Audio missing after render

After rendering a long sequence for a feature length movie, the final render is missing several areas of audio. In multiple locations, we have interviews of people and some of them for no reason do not have their audio in the render. It's just not there. It plays fine in the timeline with their audio, but once we sent it to Adobe Media Encoder, it renders it without the audio in some places. I have tried multiple render outputs and presets from h.264 to Quicktime. All of them do this.
I need a solution to this fast!
Media Encoder 2014.1
Running on a Mac with OS X Yosemite 10.10, 3.4 GHz Intel Core i7, 24 GB 1333 MHz DDR3, AMD Radeon HD 6970M 2048 MB

I have had someone else report this problem before as well. Try exporting to Pro Res and see if the audio encodes correctly.
Eric
ADK

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