I am assuming that the real problem is something else I still can't figure
Well, part of the problem is just how music is recorded, engineered and mastered these days. Generally, most pop/rock music is made to sound as loud as possible which often results in clipping and distortion.
What I would recommend, especially if you tend to listen to your music as randomly mixed playlists of artists and albums, would be to analyze your music files with MJs Audio Analyzation feature and then enable Replay Gain for playback. This will go along way in making tracks from different sources sound more similar in volume. Note, this feature won't be nearly as useful if you tend to listen to full albums rather than random mixes.
Rob