That's the problem with the crackling issue. Sometimes it won't do it, and you think you've magically found the cure to stop it, then all of a sudden it comes back.
If you get a chance, try this: unplug your instrument cable from the input jack, put it on a profile that gives you crackling, turn off your noise gates and see what kind of noise it makes with nothing plugged in.
I really hope you can solve what's causing your issues, because then maybe I can fix mine!!