Recorded an audio file using microphone via Windows Sound recorder, but has 2 channels that are slightly different. Why are they different?
I am not %100 sure, but it sounds like you are recording the file in stereo. If this is the case, then Windows Sound recorder is taking stereo input, which means it's accessing 2 AD converters which have the same input applied to them. The difference between the two signals in this case would be the noise and any offset between the two converters.

I would see if Windows Sound Recorder could make a mono recording, or else use another program to make the recording.