If you want the software to recognize the input modes, try switching them in the sound application that is installed for your Sigma High Definition Codec. Most problems are encountered when the configuration is different than the one necessary for proper run of the program. Go to System Tray, right click the Sound Icon and then access PlayBack. Make sure to choose the correct items in the list. Restart the software and it should work.
Additionally, it's possible that the WinDVR might lack support for line-in modes.