How many audio channels are you expecting?
You don't mention the type of source file you're converting from, but I hit 
this when converting some XAVC MXFs from a Sony PXW-X180, which had I believe 
four audio tracks. The resulting file was interpreted as having four mono 
tracks rather than two stereo, which was inconvenient in the NLE.

Eventually, I ended up using the -filter_complex option to do some sort of 
audio merge - I can't remember the specifics, but you may want to look at the 
"amerge" filter. But as I say, I'm not sure what your input file is and what 
you're expecting to get out. You may also be able to reject channels you're not 
interested in entirely, and end up with a stereo output file. Depends what you 
need.

P

      From: Kevin Wells <[email protected]>
 To: "[email protected]" <[email protected]> 
 Sent: Tuesday, 9 December 2014, 21:50
 Subject: [FFmpeg-user] Prores enable all audio channels on output file
   
Hi, I have seen a few posts about this previously where on the output file of a 
quicktime only the first audio channel is enabled by default, all other audio 
channels are present but disabled.I would like to have all my audio channels 
enabled by default on the output file.I am using ffmpeg 2.5 on OSX.
Kind regards.                                                 
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