Hi Peter,
MXF files are great because of the wealth of information that they can pack in to the metadata to describe the essence it carries however as a result there are a myriad of different ways of carrying audio in MXF files which will impact what is the appropriate mapping for you to output to extract the files you need.
I would recommend that you post the information you get from the source file by just running the -i command and pasting the results here for us to take a full look at.
The -map option is usually enough to allocate the mapping of your output into files, streams and channels (in that order).
e.g. 0:1:0:0:1:0
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tip – A regular gotcha for anybody dealing with numbers in this output is to remember that the first item whether it is a file, stream or channel will start from ‘0’
-Chris Oram
https://antiversal.com
Technology, Design and Development for Moving Image Creators