I would be helpful if you could upload one of the tracks making extra noises. You should be able to upload a sample here.
The track you uploaded suffers from audible clipping. There are several ways to solve this simple problem. You could turn on ReplayGain and amplitude would be lowered enough to fix it. You could also turn down the player volume. You could switch to DirectSound output and Windows would handle the clipping parts by lowering volume momentarily fixing the nasty pops. Or you can enable Advanced limited DSP to do pretty much the same with your current output mode.I noticed that Windows Media Player is especially bad with your sample file. It clips the signal while decoding and no matter how low the volume is the output sounds clipped.