What exactly are you plugging into the Line In?
The Line In is a stereo mini jack. Meaning it has 3 connections, left hot, right hot, and the common ground.
The type of connector that connects to it is a TRS (tip, ring, sleeve). Usually, tip would be Left hot, ring would be Right hot, and sleeve would be Common Ground.
If you plugged in a TS (tip, sleeve) connector to a TRS jack, the ground of the connector would be going to the Right hot and the common Ground. Since the ground doesn't carry any audio signal, you would not have anything going to the right input on the sound card.
Make sense?