I was having the same issue but with magiclantern-Nightly.2018Feb04.6D116, which is on the 6D, but found the solution here:
https://www.magiclantern.fm/forum/index.php?topic=18394.msg176331#msg176331
Have to enable to MLV_REC.mo as well.
I still would like to be able to record one channel on internal mic and another channel on external mic but cannot seem to do that on the 6D
https://www.magiclantern.fm/forum/index.php?topic=18394.msg176331#msg176331
Have to enable to MLV_REC.mo as well.
I still would like to be able to record one channel on internal mic and another channel on external mic but cannot seem to do that on the 6D