The capacitor is there because audio input of a sound card cannot see DC. By putting a capacitor there, it will cut out all the DC component, and only the AC component, the change (such as a sudden rise in voltage when diode sees the light and NOT see the light) in voltage, will be apparent. In essence you are making a differentiation circuit. That's why the peak goes to the opposite direction - charge and discharge. No, it isn't charging THAT capacitor actually....

You should be seeing more changes though, even without a capacitor.