I had this problem and I discovered if I changed the Format settings under my Built-in Output in Audio MIDI, it cleared up the sound. I had a weird double echo sound after using my ATR-2100 mic. I unplugged the mic and rebooted, but the sound distortion was still there. I changed my format to 48.0 kHZ from 44.1, which was the setting it was using.
My question is: why would using the mic change this setting for the output?
I'm new to using external mics, so my knowledge is newbie style
Looking at what I had, I'm starting to believe the sound distortion is due to having too many output and input options. I think it's just a bit too much for the computer to handle. Is your mic a Yeti as well?