Just to make sure, have you looked at Universal Control and adjusted your monitor settings? UC will affect everything monitor-related.
For S/PDIF, for example, if you don't want to hear it right away, you need to turn down the UC 9/10 faders for main, 3/4, and 5/6 (if you use all those).
With complex routing, you might want Universal Control to start on login, and use it to make sure your monitor routings are where you want them to be. The documentation is very thin on this, so you will need to experiment to see how things work.