I have the Logitech Z623 speakers. I had a crackling problem and fixed it.
Problem: Speakers were playing normally. Then, I played a song really loud (max PC and knob volumes, bass knob maxed [I think, not sure]) and noticed less than a minute afterwards that all speakers (left, right, and subwoofer) crackled when I played any audio (independent of treble/mids/bass levels) at pretty much any volume.
Solution: Switched out the 3.5mm aux cable for another one.
Hope this helps someone.