Crackling sound in some programs and not in others: what's wrong?

I am experiencing a crackling sound when I record into my Windows 10 PC Voice Recorder. The same mic and USB soundcard set up records a pure sound into Skype or Avid ProTools. I can’t figure out what goes wrong in Voice Recorder. The set up is: Zoom H4n recorder via line out into Focusrite Scarlett 2i2 sound card, via USB into my laptop.