Hopefully my original video now works...
So... this is wierd!
I started a new timeline with my footage, and resynced using my markers. Before I did this, I set my clip attributes to Audio 5.1 and each channel playing on a separate track of audio. When I dropped my clips onto the timeline and synced my audio using my markers (irrelevant) I had 4 audio tracks on the timeline (expected)
Audio 1 - mono - original camera track
Audio 2 - 5.1 - set to output L linked to Channel 1 in the wav
Audio 3 - 5.1 - set to output R linked to Channel 2 in the wav
Audio 4 - 5.1 - set to output C linked to Channel 3 in the wav
Set my Master track mixer to 6 channels and set Audio 1 track to mute, the mixer also set to None for Audio 1. Plays fine. I've got 4 tracks in my mixer which are all doing as they should; the levels meter moving in the correct channel, and the Master, set to 6 channels.
Over in the Deliver tab I play through and I have6 channels, 3 of which are playing my audio as it should. Set my Audio output channels to 6 and add to render queue. Clicking Render, I only again see 1 channel of audio playing, and when I play the file through the only channel I can hear is Audio 1 - the mono camera track! which definitely was muted!
No other channel has exported!
I tried a second time, this time deleting the mono track completely, and no audio exported at all!