I had a crackle/pop issue with the course Mourguiet attentuator in a Stereomour. It turned out to be an unsoldered connection between a resistor and the attenuator. The resistor lead was well crimped, so worked fine without noise when the course attenuator was set, but would briefly crackle/pop when switching to or from the affected attentuation setting (I think it was the -18dB position).
If in your case the crackle is particularly bad when switching to or from a certain position, then I'd focus your investigative efforts there. If it's not associated with a particular position on the attenuator, then I'd look for a loose connection somewhere close to the course attenuator that might be jostled by clicking from one position to another. The mechanical resistance of those attenuators is pretty strong and sets off a pretty big vibration in the chassis. The fact that you are now hearing the same thing when switching impedances is consistent with a loose connection -- one that is getting looser and is now affected by lesser vibrations.
You could also try to rule out the input wiring as the culprit by changing the inputs used to see if if only one is affected. Ditto for the outputs.
cheers and good luck, Derek