Are any Mute buttons flashing in the mixer?
No.
Are all channels routed to Output 1-2?
Yes.
If not are the Aux's routed to Output 1-2
Yes.
Do the "backups" for this project (in the project folder) have the same issue?
Tried a few, all with the same issue.
Have you tried switching to built-in audio and then to your audio interface again:
Logic Pro > Preferences > Audio
Yes, no change.
But I just discovered an odd thing: I turned all the audio channel Input buttons on, and suddenly my one MIDI track was playing through all of them. When I deselected each one, the audio got quieter until none were selected, and at that point I still could hear the midi, only very quietly. Isn't that unusual?
Earlier today (a couple of hours before this all happened), I went into the Environment to try and connect a channel with an aux track (I connected one virtual cable, then realized that was entirely unnecessary). I don't know if that cable could be screwing things up, but I don't know how to delete it.
Also, could the fact that I added Omnisphere yesterday have caused an isolated problem like this?