Something is messed up on your DAC. Perhaps a driver setting? Or just a borked driver?
In any case, that's almost certainly where the problem lies.
Or all of your files are messed up. But that seems unlikely. It is also quite unlikely to be a setting in MC that could be causing it, if it happens with other (unrelated) audio on the system (unless you somehow replicated the same bad setting in both MC and iTunes).
I think you messed up something in the DAC driver, or the DAC driver itself is messed up, and it is running its clock all out of whack.