I kept working at it and I think I may have found the problem…
If you noticed in my previous post, the ‘Device Properties’ were set to 24-bit, 48,000 Hz. SoundTap saves audio files at 16-bit 44,100 Hz. In my case I saved them in WAV formart. I changed by ‘Device Properties’ output to match the file settings of SoundTap.
For my Windows 10 computer the setting are under 'Manage Audio Devices' > select your playback device and click 'Properties' > click the tab 'Advanced'. Now change the 'Default Format to 16 bit, 44100 Hz (CD Quality).
I’ve recorded over an hour of audio and the problem has not happened again.
I assume - I’m guessing here - when SoundTap saves the audio file, it has to down-convert my file to the lower bitrate. That’s when the pop sound is created.
This is similar to shortening the length of an audio file (make a 70 second file 60 seconds). The more you "crunch" the file, the better chances of getting pops just like what we were experiencing.
I hope this helps someone.