A long time ago I had audio "hiccups" that were very occasional. Once an hour, once every 2 hours, etc. But mine only lasted for 1/4 to 1/2 second. I tried a lot of different things including a full reinstallation of the OS. But you have dropouts of more than 1 second. You said roughly 3 seconds. This sounds like a different problem than I had.
It's worth checking your audio Device settings:
Tools > Options > Audio > Audio Device :
Check the name of the device listed. It should be Apogee Duet2... If it's "default audio device", don't use that. Use the named device corresponding to your DAC.
Next check Device settings:
For now I would uncheck Integer Mode and uncheck exclusive access. For buffering, Hardware should be at the Hardware default. Software should start at 100 mS, but you can put it as high as 500, or 750 mS as an experiment.
After you change any of these settings, close the options windows, then restart MC.
Try playing with that for a bit and see if it helps. If it does not, I would suspect something more fundamental.
For example, thunderbolt connectors are notoriously "loose". It's sometimes a challenge to get them to fit into the port snuggly and stay there. I would be inclined to power everything down, unplug it piece by piece, and verify that I have a good connection with a good cable.
Play with the settings first. Then maybe do the hardware check, re-connect that I described above.
Good luck.
Brian.
