In a line-level audio signal, what function of voltage produces amplitude?
Between the line-in tip of the socket and the ADC there is a series capacitor which converts the square wave into what you see.

In the One Laptop per Child XO laptop, we added a way to bypass this series capacitor for DC sampling, but on typical computers this is not a design feature. On sheet 13 of the schematic look for C35, and consider the switching element over it.  The host can control the mode through software.