Hmmm. Maybe your 680 needed a power reset to recognize the change for some reason. I don't recall ever needing to so that though. Does it now work to the stereo track with STEREO REC = DIN as well? I think in addition to that setting change, you also need to set ch 5/6 back to analog to make that work.
But unless you need 8 recorded channels, you might as well record the V3 SPDIF signal to ch5/6 anyway. That way you can headphone monitor all your inputs if you like, and/or listen to a mix of all recorded channels direct out of the recorder, neither of which include the separate stereo channel.