Narwal,
I too have a MicroMega MyDac attached to a Mac Mini via a USB. I thought I would share my experience since I have a similar set up even if you resolved you issue already. I found Micro Mega to be a pretty fantastic Dac, but it can be a little temperamental for sure. I actually had no problems with connecting Mac Mini to it via USB but I had a harder time with optical. I'm speculating here, but I think as the connections get to maximum, it needs a bit more tinkering/refinement to make it happy. I heard from other owners that what else you have plugged into your USB bus is important. You basically want no other USB devices plugged into the mini particularly if you want to run 192 kHz data through it. Even which of the four USB slots you are using on the Mini can make a difference. I found the slot farthest away from the power supply of the mini to be best.
Another thing that you have to be careful about is how your components are grounded if you are using USB connectors (in that sense optical does not transmit ground between components. I have my MacMini connected to powe but not grounded. It is connected to the MyDac which is not grounded thrown AC power or any of the other two lines in. The Dac is only grounded through it's connection to the AMP which is where most audiophiles prefer to ground the system (disclaimer -- I am not an electrical engineer).
Finally, I use BitPerfect as a player on the mini to the Dac. Through it and the blog of the guy that is behind Bit Perfect, I learned that buffer size and utilization are quite important variables. Both the software in the Mini and the memory buffer in the MyDac have toalign so to speak so the data is not corrupted or lost particularly if it has to be reclocked. Long story short--I found that I can go with a much larger software buffer in BitPerfect if I use USB. But for optical I actually had the same symptoms that I think you had for USB until I played with buffer sizes on both devices. Both connections now work perfectly (my USB cable is 6' btw). Play around with that if you are still having problems.
-Dmitri
