Glad you are able to confirm that as Skype nor FreeDOS make any reference to each other in any form. Thanks for that information. :)
This is going to be a physical issue most likely unless the FreeDOS version of Skype has separate audio settings like the Windows version does. If the motherboard was replaced at a PC shop, I would explain what is happening and have them examine it to verify the cable is not damaged and is connected properly on both ends.