I don’t get any “not a valid mkv file” message but the v9.3.1 doesn’t deliver anything when I launch the muxing. There might be a change to be done with the audio file prior to the muxing step.
edit: ok, to make it work you need to open the .mov file in audacity, then export it as “wav 16 bit” (it’s the same lossless quality as the original file). You end up with a .wav file that is easily read by mkvtoolnix.