If you're bringing audio in through the analog inputs, then you've probably got the wrong audio sampling rate selected. The Sony DVMC units support 12-bit 32-Khz audio and 16-bit 48-Khz audio, as per the DV spec. If you have it capturing at 12-bit 32-Khz, then set Peak or Premiere to the higher setting, you'll get pops and stuff.
Check the light on the Analog In button. If it's green, then it's converting at 12-bit 32-Khz. If it's red, then it's 16-bit 48-Khz. To change it, press and hold the button for 3 seconds. Regardless of which setting you use, as long as your computer settings match, it'll be fine.