Adobe Media Encoder not recognizing audio

I have MXF file I need to encode on a daily basis, but AME shows there is not audio in the files. QuickTime plays (and exports) the files great with audio (showing the audio as 16-bit integer big endian) Anyway I can force AME to recognize the audio?

This is at a Television Station. Shows and Promos are digitally delived to the station in a multitude of formats to our "Master Control". They have a server that recieves the files and flips them (via Flipfactory Telestream) into a format our main HD playout server uses to playout to air. The output setting for this process can not be changed (might change in the future?).
I need the promos that these companies send. So I have to grab the flipped files from our "Master Control". The raw files that were sent are not a playable (for me) format. I can "flip" them manually using Quicktime, but I would like to be able to set up watch folders that AME can use to grab the various promos and flip them as they are recieved.
Hope this all makes sense...

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