Found the problem - solved!!!
I created 3 stereo inputs for each of my stereo pairs in the VST connections window, then I looked in the mixer and saw that the S/PDIF stereo inputs were responsive to the signals from my synth that was connected to the 3-4 inputs.
So basically DavidRavenMoon pointed the solution out, but I was sure I checked that before and the S/PDIF did not respond to any signal.
Anyway it is pretty weird, the inputs are named "Input S/PDIF X" in the Port System Name which cannot be edited, but I can change the 'Show As' value so it is ok. But very confusing however.
Happy I can use my 3-4 inputs again