Not entirely surprising. There is no single, stable way to get a Skype recording without software that “knows” how to use Skype or hardware. Skype has a nasty habit of grabbing control of the sound services in the computer and it doesn’t matter what you want at all.
I did my recording with two computers and a mixer. One computer ran Skype and the other recorded the whole show and provided music and support sounds.
People do make software to record Skype. The Pamela upper two licenses, Business and Professional will reliably record both sides of a Skype call and give you independent, high quality WAV sound tracks for each one.
http://www.pamela.biz/en/products/
There are other software products that can be used, but be careful not to get locked into MP3 sound files because of editing problems, or into a program that insists on jamming both voices onto one track.
https://forum.audacityteam.org/t/help-recording-with-a-mic-laptop-and-headphones/35068/6
Koz