If it was working before the motherboard replacement, I would have the connections checked and verified. The microphone is at the top of the LCD screen where the webcam is located and there is a cable that runs down the LCD frame, through the hinge, and to the motherboard. If that cable is damaged (it is a ZIF cable and very easy to damage) or loose, then the mic itself will not work.
Also, does Skype support FreeDOS? According to this site, it works with Windows, Mac, and Linux. FreeDOS does not fit directly into either of those categories. I'm just trying to get a better understanding of how Skype works on FreeDOS.