| You judge everything with your ears! Visual aids such as an spectrum analyzer should only be used once you are comfortable with making similar decisions with your ears. Its a creative subject, not a scientific one, and SEEING things that look wrong should only ever be a cue to listen a bit harder to the aspect in question.
The reason could be a number of things, a resonance in the room, amp, bass or your fingers. In reality most bass parts have variations like the ones you describe, but if it SOUNDS bad in those places to you as well, and compression doesn't solve it, then try listening out for those notes sounding louder than other in the room or look at your techniqe to see if you are digging in too much on certain strings/areas of the fretboard!
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