I'm running Sonar X3 Producer, upgrading to platinum later this week.
I am using a Presonus Firestudio Project as my audio device.
 
I have no problem selecting S/PDIF as an input source, but I can't seem to select it as an output source.
 
Does anyone know what could be wrong?

Check Preference - Device
 
Perhaps some input / output is not checked for Sonar to use yet.

Everything there is checked, but nothing there mentions S/PDIF.  It's all analog ins and outs.

Your S/PDIF outputs are probably listed but may be showing as numbered outputs

I would suggest checking any interface mix control software to check the routing of your audio interface - it may be setup to push a signal to your S/PDIF outputs - to you may be able to set it to here

I looked into that just now and I'm finding sources that are telling me that SPDIF is routed through outputs 9 and 10, which does make sense since it's normally an 8 channel device.
 
I'll have to look into that when I get back into the studio tomorrow.  Thanks for pointing me in that direction, I'll let you know if that solves it!
 
-Edit
 
Just got back to the studio and it does appear that for whatever reason, the Presonus Firestudio labels the SPDIF out as analog 9 and 10.
Thanks for pointing me that direction!

Awesome - glad you got it sorted