Not sure if the file type makes any difference.
It does. WAV standard (FL, FR, C, LFE, RL, RR) is different than M4A (C, FL, FR, RL, RR, LFE)
Can`t you use Foobar to convert the file? I used it convert the multi-channel wav-file to a multi-channel FLAC file.
The way I did it was to ...