Is it because the prefix, i.e. the name just before the channel indication, was different?
Since if you look at my example, the "merged" file is compiled out of files coming from different directories, but there is always a matching prefix and that's why my example works.
In my example, of course, I had to hit 6 times the "select files" button to select the files from the 6 different directories, but AudioMuxer correctly combines them together based on the prefix.
Just to be clear, in my example the matching prefixes were "PCM_Multi-16-48000", "PCM_Multi-24-48000" and "PCM_Multi-24-96000", respectively.
PM me otherwise some more details on the filenames that you have used such that I can have a better understanding of what you want to achieve.
Looks like a great project, by the way