Digital Audio Optical Input S/PDIF on Mac Mini 10.9.2

For years prior, with my MMP 15", etc. and since the fall the Mac Mini (fall '13), the setup worked flawlessly ... until recently -- since around the time updating to 10.9.2 I have had intermittant issues with the digital I/O with my Apogee Rosetta 200 until it stopped all together last week.
I have replaced or swapped out the cables first off, to no improvement -- I called Apogee and we were able to prove the input to Apogee with an Eventide Esclipse's S/PDIF output.
I called Apple and the tech and I rebooted in safemode and saw the Audio Devices pane of Audio Midi Setup and Sound neither showed the digital input/output as being active.  I sent the unit in and the logic board was replaced in view of the circumstances.
I just setup the repaired unit and now the S/PDIF out (from the Mini to the Rosetta) works -- the Sound pane shows that shows the functioning digital input however, and conspicuosly, the Audio/Midi does not (and used to).
Further, the S/PDIF in (from the Apogee to the Mac) is neither functioning nor the two panes, Audio devices and Sound, register the digial input.
Is there an issue with 10.9.2 or is it possible the one of the 1/8" analog/light pipe inputs of the Mac Mini is also not working and not determined/checked duri -- other ideas?
I have a backgorund as a Mac tech and a member of Apple Solutions Expert since back in the 90's ...

The optical digital audio input is a good way to get basic digital audio data into the Mac - assuming you have the audio in that format. Most vinyl digitizing folks do not.
The most common hardware configuration is to use your old vinyl turntable, connected to the proper phono input of a stereo (most modern stereos do not have this and you have to buy an outboard phono preamp). Then the recording (tape) output of the stereo goes to an audio interface that connects to the Mac with Firewire or USB, and not using the Mac optical input at all. There are dozens of famous makers of interfaces from a hundred dollars to thousands. For the casual user, I'd say $250 is a nice spot. You can get a stereo interface that takes analog input from your stereo, digitizes it, and send it to the Mac. It will also accept microphones, should you want. You'll need software to record and edit the audio (Audacity is free and works) and you can use iTunes to make CDs (although cumbersome).
There are interfaces that do have optical outputs that you could connect to the Mac. But since optical interfaces are rare on computers, and have many limitations, this isn't so common.
There are many tutorials on the net about digitizing LPs on computers.

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