Q: I'm getting popups asking to set mic and speakers. Please advise.

A: If you getting this message. Make sure that "Automatically detect microphone and speakers automatically" is NOT ticked and set mic and speakers manually from the drop-down menu. Click Save.
This should stop popups.
There is a 'watchdog' in recorder, it checks if recording file is created and size is growing, hence recording is in progress. When it detects that file was not created or stays small, it assumes that audio device was detected wrongly and give you the option to select it manually.

Tip: avoid changing audio device during the call.

More details in Manual 
https://voipcallrecording.com/Manual/advanced_audio_settings