Hi - just seen this...
I've been having this problem for a few days and have been searching for a solution...
The Cue mixes (headphone) mixes seem to be routed through the main output as well as output pairs 3/4,5/6, and 7/8..
This means for me I have to have the cue mixes muted when playing back the recorded tracks...
This makes things really awkward when doing overdubs / drop-ins....
I wonder if you ever figured it out?
Kind Regards Kevin