Subwoofers take a lot of time and effort to get right. It is possible for a subwoofer to be adjusted so that all music sounds great.
What you are hearing that bothers you is a peak in the response (a note or small range of notes that are louder than the others).
You can tune it out by ear if you can repeat the recording that has the booming bass and make some adjustments. Just make sure you record your current settings so you can come back to them.
Peaks are caused by phase overlap, summing with the main speakers or a position of the subwoofer that is too close to boundaries causing a peak.
Try adjusting the crossover lower as you listen to that track.
Try moving the subwoofer away from the wall, corner or surface until the peak is gone.