As the Apogee technical support site seems to be broken (and there's no mail address on their website available) I thought I might as well be posting my question here:

I have a problem with my new S I/O that when I have an analog input signal on any channel it is not being routed to the outputs. On the left meter I see without problem the input signal, also in Maestro the master mix fader shows normal output. But no output signal on the right display of the unit.

In Logic, when using a software instrument there is no problem: it's perfectly being outputted.

My output signal flow is: spdif >> tc electronics bmc-2 >> speakers.

thx in advance!

Maybe interesting for someone who runs in the same issue:

I was able to fix it by assigning in the Output routing Tab Line 1/2 (hardware output) to Software output 17-18 (Mixer1) in the Maestro software.

I'm having the same problem and a little more. My Apogee Maestro 2 shows "No Apogee system found". My Symphony Control recognises the S I/O. I am able to get o/p on headphones but no sound from either of my monitors (Yamaha HS8).
Same like you, I am able to record and listen to software instruments. I am able to record vocals but while playing there's no output either from the headphones or from the monitors. Any idea?

type : csrutil disable
when you restart your mac and hold down Control R
good luck