If you use a sound file editor to examine the flap.wav file in question, you would notice from the waveforms that one channel (left?) has a higher amplitude than the other. So this may be related to what you reported hearing.
Another possible explanation, and I’m really speculating here, is that X-Plane doesn’t simply play the sound file as is during the sim. It processes/modifies the raw sound to produce a “3D sound”. That is, depending on your position inside or outside of the aircraft, it adjusts the sound accordingly to make it sound like as if you’re hearing them from where you’re situated. If that is the case, the volume discrepancy here would be X-Plane’s own doing.
If you change your position, especially moving around outside of the C172, and keep moving the flaps, I think you will see (or hear) what I mean.