In this case make sure that you are using the correct device, go to your Control Panel\Hardware and Sound\Sound then select the recording device that you are using, the external mic or the internal one.
On WavePad select Options then the Recording tab, make sure that you are using the same device,. On the right down corner, you would found the sound mixer that would help you too. If you still getting issues, please send the information to the Tecnical Team here: https://www.nch.com.au/support/supportcontact.html?software=WavePad